From 8ac8d8a5192d79fc8c733b4c05d2453d1554b1d7 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Tue, 28 Jan 2025 16:06:40 +1000 Subject: [PATCH 01/12] ITP reader for OPLS forcefield files developed and base tested --- polytop/polytop/Angles.py | 3 + polytop/polytop/Dihedrals.py | 154 +++++++++++++---- polytop/polytop/Topology.py | 68 +++++++- tests/data/OPLS_UNK_460A12.itp | 301 +++++++++++++++++++++++++++++++++ tests/test_topology.py | 32 ++++ 5 files changed, 526 insertions(+), 32 deletions(-) create mode 100644 tests/data/OPLS_UNK_460A12.itp diff --git a/polytop/polytop/Angles.py b/polytop/polytop/Angles.py index f206e5e..29bdfb7 100644 --- a/polytop/polytop/Angles.py +++ b/polytop/polytop/Angles.py @@ -80,6 +80,9 @@ def find_bonds(atom_a: Atom, atom_b: Atom, atom_c: Atom): @staticmethod def from_atoms(atom_a: Atom, atom_b: Atom, atom_c: Atom): bond_a, bond_b = Angle.find_bonds(atom_a, atom_b, atom_c) + print(f"Bond a = {bond_a}") + print(f"Bond b = {bond_b}") + print(f"Atom a = {atom_a}, atom b = {atom_b} and atom c = {atom_c}") if bond_a is None or bond_b is None: return None return next((angle for angle in bond_a.angles if angle in bond_b.angles), None) diff --git a/polytop/polytop/Dihedrals.py b/polytop/polytop/Dihedrals.py index 933587a..adef63e 100644 --- a/polytop/polytop/Dihedrals.py +++ b/polytop/polytop/Dihedrals.py @@ -9,9 +9,23 @@ class Dihedral_type(IntEnum): """ Enum to track Dihedral types including proper (1) and improper (2). + + Proper dihedrals also include: Ryckaert-Bellemans (3), Fourier (5), + proper (multiple) (9), tabulated (8) and restricted (10). + Improper dihedrals also include: periodic improper (4). + + For more information, see + `GROMACS documentation ` + and view Table 14. """ proper = 1 improper = 2 + ryckaert_bellemans = 3 + periodic_improper = 4 + fourier = 5 + multiple = 9 + tabulated = 8 + restricted = 10 # TODO: add additional dihedral types here # but remember to update the constraint properties @@ -27,10 +41,26 @@ def is_rotational_constraint(self) -> bool: :return: True if this Dihedral is proper, and False if not. :rtype: bool """ - return self in [Dihedral_type.proper] + return self in [Dihedral_type.proper, Dihedral_type.multiple, + Dihedral_type.tabulated, Dihedral_type.restricted] @property - def is_planar_constraint(self) -> bool: # + def is_rotational_constraint_with_constants(self) -> bool: + """ + Proper dihedral: constrains torsional rotation around the BC bond, but + is defined with 6 constants increase of degrees, energy and multiplicity. + + | A -ā—ŸB | + | / | + | Cā—- D | + + :return: True if this Dihedral is proper with constants, and False if not. + :rtype: bool + """ + return self in [Dihedral_type.ryckaert_bellemans, Dihedral_type.fourier] + + @property + def is_planar_constraint(self) -> bool: """ Improper dihedral: constrains orientation of D WRT the CAB plane. In other words, the two angles are B-A-C and B-A-D @@ -43,6 +73,21 @@ def is_planar_constraint(self) -> bool: # :rtype: bool """ return self in [Dihedral_type.improper] + + @property + def is_periodic_planar_constraint(self) -> bool: + """ + Improper dihedral: constrains orientation of D WRT the CAB plane. In + other words, the two angles are B-A-C and B-A-D + + | B | + | | | + | C -ā—œAā— - D | + + :return: True if this Dihedral is periodic improper, and False if not. + :rtype: bool + """ + return self in [Dihedral_type.periodic_improper] class Dihedral: """ @@ -74,9 +119,11 @@ def __init__( atom_c: "Atom", atom_d: "Atom", dihedral_type: Dihedral_type, - phase_angle: float, - force_constant: float, - multiplicity: int, + phase_angle: float = None, + force_constant: float = None, + multiplicity: int = None, + constants: list[float] = None, + format: str = "gromos", ) -> None: """ Represents a dihedral angle formed by four atoms in a molecular system. @@ -97,6 +144,12 @@ def __init__( :type force_constant: float :param multiplicity: The multiplicity of the dihedral angle. :type multiplicity: int + :param constants: The constants used to describe the dihedra + Ryckaert-Bellemans or Fourier potential. + :type constants: list[int] + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :raises ValueError: If unable to find an Angle for the Dihedral. :raises ValueError: If an unknown Dihedral_type is provided. """ @@ -108,33 +161,63 @@ def __init__( self.phase_angle = phase_angle self.force_constant = force_constant self.multiplicity = multiplicity - if self.dihedral_type.is_rotational_constraint: - if angle_abc := Angle.from_atoms(atom_a, atom_b, atom_c): - angle_abc.dihedrals.add(self) - self.angle_a = angle_abc + self.format = format + # angles and bonds for OPLS forcefield atom order + if self.format == "opls": + if self.dihedral_type.is_rotational_constraint or self.dihedral_type.is_rotational_constraint_with_constants: + if angle_abc := Angle.from_atoms(atom_a, atom_b, atom_c): + angle_abc.dihedrals.add(self) + self.angle_a = angle_abc + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_bcd := Angle.from_atoms(atom_b, atom_c, atom_d): + angle_bcd.dihedrals.add(self) + self.angle_b = angle_bcd + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + elif self.dihedral_type.is_planar_constraint or self.dihedral_type.is_periodic_planar_constraint: + if angle_abc := Angle.from_atoms(atom_a, atom_b, atom_c): + angle_abc.dihedrals.add(self) + self.angle_a = angle_abc + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_abd := Angle.from_atoms(atom_a, atom_b, atom_d): + angle_abd.dihedrals.add(self) + self.angle_b = angle_abd + else: + raise ValueError(f"Could not find angle for dihedral: {self}") else: - raise ValueError(f"Could not find angle for dihedral: {self}") - if angle_bcd := Angle.from_atoms(atom_b, atom_c, atom_d): - angle_bcd.dihedrals.add(self) - self.angle_b = angle_bcd - else: - raise ValueError(f"Could not find angle for dihedral: {self}") - elif self.dihedral_type.is_planar_constraint: - if angle_bac := Angle.from_atoms(atom_b, atom_a, atom_c): - angle_bac.dihedrals.add(self) - self.angle_a = angle_bac + raise ValueError(f"Unknown dihedral type: {dihedral_type}") + + # angles and bonds for GROMOS forcefield atom order + if self.format == "gromos": + if self.dihedral_type.is_rotational_constraint or self.dihedral_type.is_rotational_constraint_with_constants: + if angle_abc := Angle.from_atoms(atom_a, atom_b, atom_c): + angle_abc.dihedrals.add(self) + self.angle_a = angle_abc + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_bcd := Angle.from_atoms(atom_b, atom_c, atom_d): + angle_bcd.dihedrals.add(self) + self.angle_b = angle_bcd + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + elif self.dihedral_type.is_planar_constraint or self.dihedral_type.is_periodic_planar_constraint: + if angle_bac := Angle.from_atoms(atom_b, atom_a, atom_c): + angle_bac.dihedrals.add(self) + self.angle_a = angle_bac + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_bad := Angle.from_atoms(atom_b, atom_a, atom_d): + angle_bad.dihedrals.add(self) + self.angle_b = angle_bad + else: + raise ValueError(f"Could not find angle for dihedral: {self}") else: - raise ValueError(f"Could not find angle for dihedral: {self}") - if angle_bad := Angle.from_atoms(atom_b, atom_a, atom_d): - angle_bad.dihedrals.add(self) - self.angle_b = angle_bad - else: - raise ValueError(f"Could not find angle for dihedral: {self}") - else: - raise ValueError(f"Unknown dihedral type: {dihedral_type}") + raise ValueError(f"Unknown dihedral type: {dihedral_type}") @classmethod - def from_line(cls, line: str, atoms) -> Dihedral: + def from_line(cls, line: str, atoms, format: str = "gromos") -> Dihedral: """ Class method to construct Dihedral from the line of an ITP file and a list of all Atom's present in the topology. @@ -154,13 +237,22 @@ def from_line(cls, line: str, atoms) -> Dihedral: dihedral_type = Dihedral_type(int(parts[4])) phase_angle = float(parts[5]) force_constant = float(parts[6]) - if dihedral_type.is_rotational_constraint: + constants = [] + if dihedral_type.is_rotational_constraint or dihedral_type.is_periodic_planar_constraint: multiplicity = int(parts[7]) - elif dihedral_type.is_planar_constraint: + elif dihedral_type.is_planar_constraint or dihedral_type.is_rotational_constraint_with_constants: multiplicity = None # multiplicity is not required for improper dihedrals else: warnings.warn(f"Unknown dihedral type: {dihedral_type}") + if dihedral_type.is_rotational_constraint_with_constants: + constants = [float(parts[5]), float(parts[6]), float(parts[7]), float(parts[8]), float(parts[9])] + if len(parts) > 10: # only append sixth constant if available (in Rychaert-Bellemans, but not in Fourier dihedral type) + constants.append(float(parts[10])) + # set angle and force to None + phase_angle = None + force_constant = None + return cls( atom_a, atom_b, @@ -170,6 +262,8 @@ def from_line(cls, line: str, atoms) -> Dihedral: phase_angle, force_constant, multiplicity, + constants, + format ) @staticmethod diff --git a/polytop/polytop/Topology.py b/polytop/polytop/Topology.py index 07602a2..5ee7bbe 100644 --- a/polytop/polytop/Topology.py +++ b/polytop/polytop/Topology.py @@ -261,12 +261,12 @@ def _rearrange_atoms(self): @classmethod def from_ITP(cls, file_path: str, preprocess=None) -> Topology: """ - Class method to create a Topology object from a GROMACS ITP file. + Class method to create a Topology object from a GROMOS forcefield ITP file. Note: this function does not explicitly check that moleculetype.nrexcl = number of exclusions associated with atoms. - :param file_path: the path to the GROMACS ITP file. + :param file_path: the path to the GROMOS ITP file. :type file_path: str :param preprocess: function to preprocess the topology, that must accept the section and line as arguments in that order, @@ -322,6 +322,70 @@ def from_ITP(cls, file_path: str, preprocess=None) -> Topology: warnings.warn(f"Unknown section {section} in {file_path}") return cls(atoms, preamble, molecule_type) + @classmethod + def from_OPLS_ITP(cls, file_path: str, preprocess=None) -> Topology: + """ + Class method to create a Topology object from an OPLS forcefield ITP file. + + Note: this function does not explicitly check that + moleculetype.nrexcl = number of exclusions associated with atoms. + + :param file_path: the path to the OPLS ITP file. + :type file_path: str + :param preprocess: function to preprocess the topology, that must + accept the section and line as arguments in that order, + defaults to None. + :type preprocess: lambda function, optional + :return: the created Topology object. + :rtype: Topology + """ + + with open(file_path, "r") as f: + lines = f.readlines() + + preamble = [] + molecule_type = None + atoms = [] + + section = None + for line in lines: + line = line.strip() + if not line or line.startswith(";"): + if section is None: + preamble.append(line) + continue + if line.startswith("["): + section = line.strip("[] ").lower() + continue + if preprocess is not None: + line = preprocess(section, line) + if section == "moleculetype": + molecule_type = MoleculeType.from_line(line) + continue + elif section == "atoms": + atom = Atom.from_line(line) + # check for issues with atom type or name + atom.element #TODO: add support OR remove this check? + atoms.append(atom) + elif section == "bonds": + Bond.from_line(line, atoms) + elif section == "angles": + Angle.from_line(line, atoms) + elif section == "pairs": + Pair.from_line(line, atoms) + elif section == "dihedrals": + Dihedral.from_line(line, atoms, format="opls") + elif section == "exclusions": + if len(line.split()) > 2: + for second_atom in range(1, len(line.split())): + indexes = [0, second_atom] + Exclusion.from_line(line, atoms, indexes=indexes) + else: + Exclusion.from_line(line, atoms) + else: + warnings.warn(f"Unknown section {section} in {file_path}") + return cls(atoms, preamble, molecule_type) + def to_ITP(self, file_path: str): """ Write the Topology to a GROMACS ITP file. diff --git a/tests/data/OPLS_UNK_460A12.itp b/tests/data/OPLS_UNK_460A12.itp new file mode 100644 index 0000000..28860e9 --- /dev/null +++ b/tests/data/OPLS_UNK_460A12.itp @@ -0,0 +1,301 @@ +[ atoms ] +; nr type resnr residue atom cgnr charge mass + 1 opls_800 1 UNK C00 1 -0.2389 12.0110 + 2 opls_801 1 UNK C01 1 -0.1779 12.0110 + 3 opls_802 1 UNK C02 1 -0.1660 12.0110 + 4 opls_803 1 UNK C03 1 -0.1329 12.0110 + 5 opls_804 1 UNK C04 1 -0.1639 12.0110 + 6 opls_805 1 UNK C05 1 -0.2400 12.0110 + 7 opls_806 1 UNK C06 1 0.6111 12.0110 + 8 opls_807 1 UNK O07 1 -0.4483 15.9990 + 9 opls_808 1 UNK N08 1 -1.1135 14.0070 + 10 opls_809 1 UNK C09 1 0.2101 12.0110 + 11 opls_810 1 UNK C0A 1 -0.2525 12.0110 + 12 opls_811 1 UNK C0B 1 -0.2621 12.0110 + 13 opls_812 1 UNK H0C 1 0.0828 1.0080 + 14 opls_813 1 UNK H0D 1 0.0828 1.0080 + 15 opls_814 1 UNK H0E 1 0.0828 1.0080 + 16 opls_815 1 UNK H0F 1 0.0871 1.0080 + 17 opls_816 1 UNK H0G 1 0.0871 1.0080 + 18 opls_817 1 UNK H0H 1 0.1074 1.0080 + 19 opls_818 1 UNK H0I 1 0.1074 1.0080 + 20 opls_819 1 UNK H0J 1 0.1054 1.0080 + 21 opls_820 1 UNK H0K 1 0.0888 1.0080 + 22 opls_821 1 UNK H0M 1 0.0888 1.0080 + 23 opls_822 1 UNK H0N 1 0.0886 1.0080 + 24 opls_823 1 UNK H0O 1 0.0886 1.0080 + 25 opls_824 1 UNK H0P 1 0.0886 1.0080 + 26 opls_825 1 UNK H0Q 1 0.5084 1.0080 + 27 opls_826 1 UNK H0R 1 0.1356 1.0080 + 28 opls_827 1 UNK H0S 1 0.0906 1.0080 + 29 opls_828 1 UNK H0T 1 0.0906 1.0080 + 30 opls_829 1 UNK H0U 1 0.0906 1.0080 + 31 opls_830 1 UNK H0V 1 0.0908 1.0080 + 32 opls_831 1 UNK H0W 1 0.0908 1.0080 + 33 opls_832 1 UNK H0X 2 0.0908 1.0080 +[ bonds ] + 2 1 1 0.1529 224262.400 + 3 2 1 0.1529 224262.400 + 4 3 1 0.1529 224262.400 + 5 4 1 0.1529 224262.400 + 6 5 1 0.1529 224262.400 + 7 4 1 0.1522 265265.600 + 8 7 1 0.1229 476976.000 + 9 7 1 0.1335 410032.000 + 10 9 1 0.1449 282001.600 + 11 10 1 0.1529 224262.400 + 12 10 1 0.1529 224262.400 + 13 1 1 0.1090 284512.000 + 14 1 1 0.1090 284512.000 + 15 1 1 0.1090 284512.000 + 16 2 1 0.1090 284512.000 + 17 2 1 0.1090 284512.000 + 18 3 1 0.1090 284512.000 + 19 3 1 0.1090 284512.000 + 20 4 1 0.1090 284512.000 + 21 5 1 0.1090 284512.000 + 22 5 1 0.1090 284512.000 + 23 6 1 0.1090 284512.000 + 24 6 1 0.1090 284512.000 + 25 6 1 0.1090 284512.000 + 26 9 1 0.1010 363171.200 + 27 10 1 0.1090 284512.000 + 28 11 1 0.1090 284512.000 + 29 11 1 0.1090 284512.000 + 30 11 1 0.1090 284512.000 + 31 12 1 0.1090 284512.000 + 32 12 1 0.1090 284512.000 + 33 12 1 0.1090 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-0.000 -0.000 0.000 + 8 7 4 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 + +[ pairs ] + 1 4 1 + 2 5 1 + 3 6 1 + 2 7 1 + 3 8 1 + 3 9 1 + 6 7 1 + 5 8 1 + 5 9 1 + 4 10 1 + 3 13 1 + 3 14 1 + 8 10 1 + 7 11 1 + 3 15 1 + 7 12 1 + 1 18 1 + 4 16 1 + 1 19 1 + 4 17 1 + 2 20 1 + 5 18 1 + 5 19 1 + 3 21 1 + 7 18 1 + 3 22 1 + 7 19 1 + 6 20 1 + 4 23 1 + 8 20 1 + 7 21 1 + 4 24 1 + 13 16 1 + 9 20 1 + 7 22 1 + 4 25 1 + 14 16 1 + 13 17 1 + 4 26 1 + 15 16 1 + 14 17 1 + 15 17 1 + 16 18 1 + 8 26 1 + 7 27 1 + 17 18 1 + 16 19 1 + 17 19 1 + 11 26 1 + 9 28 1 + 18 20 1 + 12 26 1 + 9 29 1 + 19 20 1 + 9 30 1 + 12 28 1 + 9 31 1 + 20 21 1 + 12 29 1 + 9 32 1 + 20 22 1 + 12 30 1 + 11 31 1 + 9 33 1 + 11 32 1 + 21 23 1 + 11 33 1 + 22 23 1 + 21 24 1 + 22 24 1 + 21 25 1 + 22 25 1 + 26 27 1 + 27 28 1 + 27 29 1 + 27 30 1 + 27 31 1 + 27 32 1 + 27 33 1 diff --git a/tests/test_topology.py b/tests/test_topology.py index 4906e41..2493444 100644 --- a/tests/test_topology.py +++ b/tests/test_topology.py @@ -129,6 +129,38 @@ def test_topology_auto_rename_atoms(data_dir: Path, output_dir: Path): assert arg_max_atom_index["N"] == 4 assert arg_max_atom_index["O"] == 2 +def test_topology_OPLS_parser(data_dir: Path, output_dir: Path): + opls = Topology.from_OPLS_ITP(data_dir/"OPLS_UNK_460A12.itp") + opls.to_ITP(output_dir/"OPLS_topology.itp") + # opls_new = Topology.from_OPLS_ITP(output_dir/"OPLS_topology.itp") + + # def same_properties(atom_a, atom_b)-> bool: + # if atom.atom_type != new_atom.atom_type: + # return False + # if atom.residue_name != new_atom.residue_name: + # return False + # if atom.residue_id != new_atom.residue_id: + # return False + # if atom.partial_charge != new_atom.partial_charge: + # return False + # if atom.mass != new_atom.mass: + # return False + # return True + + # atoms = opls.atoms + # new_atoms = opls_new.atoms + # assert len(atoms) == len(new_atoms) + # for i in range(len(atoms)): + # atom = atoms[i] + # new_atom = new_atoms[-i-1] + # assert same_properties(atom, new_atom) + # for atom in atom.bond_neighbours(): + # assert any(same_properties(atom, rev_atom) for rev_atom in new_atom.bond_neighbours()) + # for atom in atom.angle_neighbours(): + # assert any(same_properties(atom, rev_atom) for rev_atom in new_atom.angle_neighbours()) + # for atom in atom.dihedral_neighbours(): + # assert any(same_properties(atom, rev_atom) for rev_atom in new_atom.dihedral_neighbours()) + @pytest.mark.xfail(reason="New method of separating atoms into unique charge groups and renumbering them before saving to ITP is breaking this test.") def test_reverse_topology(data_dir: Path, output_dir: Path): glu = Topology.from_ITP(data_dir/"glutamine.itp") From 3925fe51a9048283c18a124558c3227b2b0d70c0 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Tue, 28 Jan 2025 16:16:51 +1000 Subject: [PATCH 02/12] Modify 'from_ITP()' reader to use a new 'format' optional argument - this enables the same function to handle all forcefield formats and direct resolving format differences (i.e. in the way dihedrals may be specified) to lower level class methods --- polytop/polytop/Topology.py | 73 +++---------------------------------- tests/test_topology.py | 2 +- 2 files changed, 7 insertions(+), 68 deletions(-) diff --git a/polytop/polytop/Topology.py b/polytop/polytop/Topology.py index 5ee7bbe..b6c8e7d 100644 --- a/polytop/polytop/Topology.py +++ b/polytop/polytop/Topology.py @@ -259,9 +259,9 @@ def _rearrange_atoms(self): return atoms @classmethod - def from_ITP(cls, file_path: str, preprocess=None) -> Topology: + def from_ITP(cls, file_path: str, preprocess=None, format: str = "gromos") -> Topology: """ - Class method to create a Topology object from a GROMOS forcefield ITP file. + Class method to create a Topology object from an ITP file. Note: this function does not explicitly check that moleculetype.nrexcl = number of exclusions associated with atoms. @@ -272,6 +272,9 @@ def from_ITP(cls, file_path: str, preprocess=None) -> Topology: accept the section and line as arguments in that order, defaults to None. :type preprocess: lambda function, optional + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: the created Topology object. :rtype: Topology """ @@ -310,71 +313,7 @@ def from_ITP(cls, file_path: str, preprocess=None) -> Topology: elif section == "pairs": Pair.from_line(line, atoms) elif section == "dihedrals": - Dihedral.from_line(line, atoms) - elif section == "exclusions": - if len(line.split()) > 2: - for second_atom in range(1, len(line.split())): - indexes = [0, second_atom] - Exclusion.from_line(line, atoms, indexes=indexes) - else: - Exclusion.from_line(line, atoms) - else: - warnings.warn(f"Unknown section {section} in {file_path}") - return cls(atoms, preamble, molecule_type) - - @classmethod - def from_OPLS_ITP(cls, file_path: str, preprocess=None) -> Topology: - """ - Class method to create a Topology object from an OPLS forcefield ITP file. - - Note: this function does not explicitly check that - moleculetype.nrexcl = number of exclusions associated with atoms. - - :param file_path: the path to the OPLS ITP file. - :type file_path: str - :param preprocess: function to preprocess the topology, that must - accept the section and line as arguments in that order, - defaults to None. - :type preprocess: lambda function, optional - :return: the created Topology object. - :rtype: Topology - """ - - with open(file_path, "r") as f: - lines = f.readlines() - - preamble = [] - molecule_type = None - atoms = [] - - section = None - for line in lines: - line = line.strip() - if not line or line.startswith(";"): - if section is None: - preamble.append(line) - continue - if line.startswith("["): - section = line.strip("[] ").lower() - continue - if preprocess is not None: - line = preprocess(section, line) - if section == "moleculetype": - molecule_type = MoleculeType.from_line(line) - continue - elif section == "atoms": - atom = Atom.from_line(line) - # check for issues with atom type or name - atom.element #TODO: add support OR remove this check? - atoms.append(atom) - elif section == "bonds": - Bond.from_line(line, atoms) - elif section == "angles": - Angle.from_line(line, atoms) - elif section == "pairs": - Pair.from_line(line, atoms) - elif section == "dihedrals": - Dihedral.from_line(line, atoms, format="opls") + Dihedral.from_line(line, atoms, format=format) elif section == "exclusions": if len(line.split()) > 2: for second_atom in range(1, len(line.split())): diff --git a/tests/test_topology.py b/tests/test_topology.py index 2493444..e4b91e4 100644 --- a/tests/test_topology.py +++ b/tests/test_topology.py @@ -130,7 +130,7 @@ def test_topology_auto_rename_atoms(data_dir: Path, output_dir: Path): assert arg_max_atom_index["O"] == 2 def test_topology_OPLS_parser(data_dir: Path, output_dir: Path): - opls = Topology.from_OPLS_ITP(data_dir/"OPLS_UNK_460A12.itp") + opls = Topology.from_ITP(data_dir/"OPLS_UNK_460A12.itp", format="opls") opls.to_ITP(output_dir/"OPLS_topology.itp") # opls_new = Topology.from_OPLS_ITP(output_dir/"OPLS_topology.itp") From e5e7959dab3c09ab047e207e4c89ac5ad5790dab Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Tue, 28 Jan 2025 16:23:12 +1000 Subject: [PATCH 03/12] Specify that the Topology to_ITP() function should only include '[ moleculetype ]' in the output ITP if it has a value in the Topology - writing of 'None' if there was no attribute was causing issues when re-reading in an ITP --- polytop/polytop/Topology.py | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/polytop/polytop/Topology.py b/polytop/polytop/Topology.py index b6c8e7d..d918c0e 100644 --- a/polytop/polytop/Topology.py +++ b/polytop/polytop/Topology.py @@ -325,13 +325,16 @@ def from_ITP(cls, file_path: str, preprocess=None, format: str = "gromos") -> To warnings.warn(f"Unknown section {section} in {file_path}") return cls(atoms, preamble, molecule_type) - def to_ITP(self, file_path: str): + def to_ITP(self, file_path: str, format: str = "gromos"): """ - Write the Topology to a GROMACS ITP file. + Write the Topology to a GROMACS ITP file of the desired forcefield format. :param file_path: the path to and the desired name of the GROMACS ITP file. :type file_path: str + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. """ with open(file_path, "w") as f: if self.title: @@ -344,9 +347,10 @@ def to_ITP(self, file_path: str): f.write(line + "\n") else: f.write("; " + line + "\n") - - f.write("\n[ moleculetype ]\n") - f.write(str(self.molecule_type) + "\n") + + if self.molecule_type is not None: + f.write("\n[ moleculetype ]\n") + f.write(str(self.molecule_type) + "\n") f.write("[ atoms ]\n") self.atoms = self._rearrange_atoms() From 8ef299daabd31e8c87ffdcb95cd9d2546907d3c6 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Tue, 28 Jan 2025 17:06:08 +1000 Subject: [PATCH 04/12] ITP writer now supportive of OPLS forcefield format developed and base tested - mainly via expansion of Dihedral.__str__ representation to display constants when written to ITP file if the dihedral type specifies it --- polytop/polytop/Angles.py | 3 -- polytop/polytop/Dihedrals.py | 13 +++++---- polytop/polytop/Topology.py | 8 +++--- tests/test_topology.py | 56 ++++++++++++++++++------------------ 4 files changed, 40 insertions(+), 40 deletions(-) diff --git a/polytop/polytop/Angles.py b/polytop/polytop/Angles.py index 29bdfb7..f206e5e 100644 --- a/polytop/polytop/Angles.py +++ b/polytop/polytop/Angles.py @@ -80,9 +80,6 @@ def find_bonds(atom_a: Atom, atom_b: Atom, atom_c: Atom): @staticmethod def from_atoms(atom_a: Atom, atom_b: Atom, atom_c: Atom): bond_a, bond_b = Angle.find_bonds(atom_a, atom_b, atom_c) - print(f"Bond a = {bond_a}") - print(f"Bond b = {bond_b}") - print(f"Atom a = {atom_a}, atom b = {atom_b} and atom c = {atom_c}") if bond_a is None or bond_b is None: return None return next((angle for angle in bond_a.angles if angle in bond_b.angles), None) diff --git a/polytop/polytop/Dihedrals.py b/polytop/polytop/Dihedrals.py index adef63e..8f74d13 100644 --- a/polytop/polytop/Dihedrals.py +++ b/polytop/polytop/Dihedrals.py @@ -161,6 +161,7 @@ def __init__( self.phase_angle = phase_angle self.force_constant = force_constant self.multiplicity = multiplicity + self.constants = constants self.format = format # angles and bonds for OPLS forcefield atom order if self.format == "opls": @@ -397,22 +398,24 @@ def clone_dihedral_changing(self, from_atom: "Atom", to_atom: "Atom") -> Dihedra :rtype: Dihedral """ if self.atom_a == from_atom: - new_dihedral = Dihedral(to_atom, self.atom_b, self.atom_c, self.atom_d, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity) + new_dihedral = Dihedral(to_atom, self.atom_b, self.atom_c, self.atom_d, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity, self.constants, self.format) elif self.atom_b == from_atom: - new_dihedral = Dihedral(self.atom_a, to_atom, self.atom_c, self.atom_d, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity) + new_dihedral = Dihedral(self.atom_a, to_atom, self.atom_c, self.atom_d, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity, self.constants, self.format) elif self.atom_c == from_atom: - new_dihedral = Dihedral(self.atom_a, self.atom_b, to_atom, self.atom_d, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity) + new_dihedral = Dihedral(self.atom_a, self.atom_b, to_atom, self.atom_d, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity, self.constants, self.format) elif self.atom_d == from_atom: - new_dihedral = Dihedral(self.atom_a, self.atom_b, self.atom_c, to_atom, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity) + new_dihedral = Dihedral(self.atom_a, self.atom_b, self.atom_c, to_atom, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity, self.constants, self.format) else: raise ValueError(f"Atom {from_atom} is not in dihedral {self}") return new_dihedral def __str__(self): - if self.dihedral_type.is_rotational_constraint: + if self.dihedral_type.is_rotational_constraint or self.dihedral_type.is_periodic_planar_constraint: return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.atom_d.atom_id:>5} {self.dihedral_type:>5} {self.phase_angle:>10.4f} {self.force_constant:.4e} {self.multiplicity:>5}" elif self.dihedral_type.is_planar_constraint: return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.atom_d.atom_id:>5} {self.dihedral_type:>5} {self.phase_angle:>10.4f} {self.force_constant:.4e}" + elif self.dihedral_type.is_rotational_constraint_with_constants: + return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.atom_d.atom_id:>5} {self.dihedral_type:>5} {self.constants[0]:>10.3f} {self.constants[1]:>10.3f} {self.constants[2]:>10.3f} {self.constants[3]:>10.3f} {self.constants[4]:>10.3f} {self.constants[5]:>10.3f}" def __repr__(self) -> str: return f"Dihedral({self.atom_a.atom_id}, {self.atom_b.atom_id}, {self.atom_c.atom_id}, {self.atom_d.atom_id})" diff --git a/polytop/polytop/Topology.py b/polytop/polytop/Topology.py index d918c0e..b154c06 100644 --- a/polytop/polytop/Topology.py +++ b/polytop/polytop/Topology.py @@ -370,18 +370,18 @@ def to_ITP(self, file_path: str, format: str = "gromos"): f.write(str(angle) + "\n") if any( - dihedral.dihedral_type.is_planar_constraint + dihedral.dihedral_type.is_planar_constraint or dihedral.dihedral_type.is_periodic_planar_constraint for dihedral in self.dihedrals ): f.write("\n[ dihedrals ]\n") - f.write("; GROMOS improper dihedrals\n") + f.write("; improper dihedrals\n") for dihedral in self.dihedrals: - if dihedral.dihedral_type.is_planar_constraint: + if dihedral.dihedral_type.is_planar_constraint or dihedral.dihedral_type.is_periodic_planar_constraint: f.write(str(dihedral) + "\n") f.write("\n[ dihedrals ]\n") for dihedral in self.dihedrals: - if dihedral.dihedral_type.is_rotational_constraint: + if dihedral.dihedral_type.is_rotational_constraint or dihedral.dihedral_type.is_rotational_constraint_with_constants: f.write(str(dihedral) + "\n") f.write("\n[ exclusions ]\n") diff --git a/tests/test_topology.py b/tests/test_topology.py index e4b91e4..4f4632a 100644 --- a/tests/test_topology.py +++ b/tests/test_topology.py @@ -131,35 +131,35 @@ def test_topology_auto_rename_atoms(data_dir: Path, output_dir: Path): def test_topology_OPLS_parser(data_dir: Path, output_dir: Path): opls = Topology.from_ITP(data_dir/"OPLS_UNK_460A12.itp", format="opls") - opls.to_ITP(output_dir/"OPLS_topology.itp") - # opls_new = Topology.from_OPLS_ITP(output_dir/"OPLS_topology.itp") - - # def same_properties(atom_a, atom_b)-> bool: - # if atom.atom_type != new_atom.atom_type: - # return False - # if atom.residue_name != new_atom.residue_name: - # return False - # if atom.residue_id != new_atom.residue_id: - # return False - # if atom.partial_charge != new_atom.partial_charge: - # return False - # if atom.mass != new_atom.mass: - # return False - # return True + opls.to_ITP(output_dir/"OPLS_topology.itp", format="opls") + opls_new = Topology.from_ITP(output_dir/"OPLS_topology.itp", format="opls") + + def same_properties(atom_a, atom_b)-> bool: + if atom_a.atom_type != atom_b.atom_type: + return False + if atom_a.residue_name != atom_b.residue_name: + return False + if atom_a.residue_id != atom_b.residue_id: + return False + if atom_a.partial_charge != atom_b.partial_charge: + return False + if atom_a.mass != atom_b.mass: + return False + return True - # atoms = opls.atoms - # new_atoms = opls_new.atoms - # assert len(atoms) == len(new_atoms) - # for i in range(len(atoms)): - # atom = atoms[i] - # new_atom = new_atoms[-i-1] - # assert same_properties(atom, new_atom) - # for atom in atom.bond_neighbours(): - # assert any(same_properties(atom, rev_atom) for rev_atom in new_atom.bond_neighbours()) - # for atom in atom.angle_neighbours(): - # assert any(same_properties(atom, rev_atom) for rev_atom in new_atom.angle_neighbours()) - # for atom in atom.dihedral_neighbours(): - # assert any(same_properties(atom, rev_atom) for rev_atom in new_atom.dihedral_neighbours()) + atoms = opls.atoms + new_atoms = opls_new.atoms + assert len(atoms) == len(new_atoms) + for i in range(len(atoms)): + atom = atoms[i] + new_atom = new_atoms[i] + assert same_properties(atom, new_atom) + for a in atom.bond_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.bond_neighbours()) + for a in atom.angle_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.angle_neighbours()) + for a in atom.dihedral_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.dihedral_neighbours()) @pytest.mark.xfail(reason="New method of separating atoms into unique charge groups and renumbering them before saving to ITP is breaking this test.") def test_reverse_topology(data_dir: Path, output_dir: Path): From 663dd86c79a4eed1568c7989f7266fd30ab47d31 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Wed, 29 Jan 2025 11:46:04 +1000 Subject: [PATCH 05/12] ITP reader and writer now both supportive of CHARMM forcefield format and base tested - via expansion of Dihedral, Bond and Angle classes from_line() methods and __str__ representations. Also added an additional test to check that the from_ITP method rejects invalid 'format' argument strings --- polytop/polytop/Angles.py | 38 ++++- polytop/polytop/Atoms.py | 2 +- polytop/polytop/Bonds.py | 25 +++- polytop/polytop/Dihedrals.py | 21 ++- polytop/polytop/Topology.py | 7 +- tests/data/CHARMM_pnipam_gmx.itp | 243 +++++++++++++++++++++++++++++++ tests/test_topology.py | 36 +++++ 7 files changed, 352 insertions(+), 20 deletions(-) create mode 100644 tests/data/CHARMM_pnipam_gmx.itp diff --git a/polytop/polytop/Angles.py b/polytop/polytop/Angles.py index f206e5e..75e1c3e 100644 --- a/polytop/polytop/Angles.py +++ b/polytop/polytop/Angles.py @@ -26,7 +26,8 @@ class Angle: B and atoms B and C """ def __init__(self, atom_a: Atom, atom_b: Atom, atom_c: Atom, - angle_type: int, angle_value: float, force_constant: float) -> None: + angle_type: int, angle_value: float, force_constant: float, + format: str = "gromos") -> None: """ Represents an angle between three atoms in a molecular system. @@ -42,6 +43,9 @@ def __init__(self, atom_a: Atom, atom_b: Atom, atom_c: Atom, :type angle_value: float :param force_constant: The force constant associated with the angle. :type force_constant: float + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :raises ValueError: If there are not bonds present between atoms A and B and atoms B and C """ @@ -59,17 +63,36 @@ def __init__(self, atom_a: Atom, atom_b: Atom, atom_c: Atom, self.bond_ab.angles.add(self) self.bond_bc.angles.add(self) self.dihedrals = set() + self.format = format @classmethod - def from_line(cls, line: str, atoms): + def from_line(cls, line: str, atoms, format: str = "gromos") -> Angle: + """ + Class method to construct Angle from the line of an ITP file and a + list of all Atom's present in the topology. + + :param line: the ITP file line + :type line: str + :param atoms: list of all Atoms in the Topology + :type atoms: List[Atom] + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. + :return: the new Angle + :rtype: Angle + """ parts = line.split() atom_a = atoms[int(parts[0]) - 1] atom_b = atoms[int(parts[1]) - 1] atom_c = atoms[int(parts[2]) - 1] angle_type = int(parts[3]) - angle_value = float(parts[4]) - force_constant = float(parts[5]) - return cls(atom_a, atom_b, atom_c, angle_type, angle_value, force_constant) + if format=="charmm": + angle_value = None + force_constant = None + else: + angle_value = float(parts[4]) + force_constant = float(parts[5]) + return cls(atom_a, atom_b, atom_c, angle_type, angle_value, force_constant, format) @staticmethod def find_bonds(atom_a: Atom, atom_b: Atom, atom_c: Atom): @@ -151,7 +174,10 @@ def remove(self): self.bond_bc.angles.remove(self) def __str__(self): - return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.angle_type:>5} {self.angle_value:>10.4f} {self.force_constant:.4e}" + if self.format == "charmm": + return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.angle_type:>5}" + else: + return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.angle_type:>5} {self.angle_value:>10.4f} {self.force_constant:.4e}" def __repr__(self) -> str: return f"Angle({self.atom_a.atom_id}, {self.atom_b.atom_id}, {self.atom_c.atom_id})" diff --git a/polytop/polytop/Atoms.py b/polytop/polytop/Atoms.py index d763744..7e9c066 100644 --- a/polytop/polytop/Atoms.py +++ b/polytop/polytop/Atoms.py @@ -134,7 +134,7 @@ def element(self) -> str: element_name = element_name[0] return element_name - #TO DO: deconvulute following 3 functions, and atom_name, atom_id and index properties... + #TODO: deconvulute following 3 functions, and atom_name, atom_id and index properties... @element.setter def element(self, value: str): """ diff --git a/polytop/polytop/Bonds.py b/polytop/polytop/Bonds.py index b6f665d..d03b0b3 100644 --- a/polytop/polytop/Bonds.py +++ b/polytop/polytop/Bonds.py @@ -28,6 +28,7 @@ def __init__( bond_length: float, force_constant: float, order: int = 1, + format: str = "gromos" ) -> None: """ Represents a bond between two atoms in a molecular system. @@ -44,6 +45,9 @@ def __init__( :type force_constant: float :param order: The bond order, defaults to 1 (single bond) :type order: int, optional + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :raises ValueError: if either atom_a or atom_b are None """ if atom_a is None or atom_b is None: @@ -59,9 +63,10 @@ def __init__( atom_b.bonds.add(self) self.order = order self.angles = set() + self.format = format @classmethod - def from_line(cls, line: str, atoms: List["Atom"]) -> Bond: + def from_line(cls, line: str, atoms: List["Atom"], format: str = "gromos") -> Bond: """ Class method to construct Bond from the line of an ITP file and a list of all Atom's present in the topology. @@ -70,6 +75,9 @@ def from_line(cls, line: str, atoms: List["Atom"]) -> Bond: :type line: str :param atoms: list of all Atoms in the Topology :type atoms: List[Atom] + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: the new Bond :rtype: Bond """ @@ -77,10 +85,14 @@ def from_line(cls, line: str, atoms: List["Atom"]) -> Bond: atom_a = atoms[int(parts[0]) - 1] atom_b = atoms[int(parts[1]) - 1] bond_type = int(parts[2]) - bond_length = float(parts[3]) - force_constant = float(parts[4]) + if format=="charmm": + bond_length = None + force_constant = None + else: + bond_length = float(parts[3]) + force_constant = float(parts[4]) - return cls(atom_a, atom_b, bond_type, bond_length, force_constant) + return cls(atom_a, atom_b, bond_type, bond_length, force_constant, format=format) @staticmethod def from_atoms(atom_a: "Atom", atom_b: "Atom") -> Bond: @@ -218,7 +230,10 @@ def remove(self): self.atom_b.bonds.remove(self) def __str__(self): - return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.bond_type:>5} {self.bond_length:>10.4f} {self.force_constant:.4e}" + if self.format == "charmm": + return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.bond_type:>5}" + else: + return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.bond_type:>5} {self.bond_length:>10.4f} {self.force_constant:.4e}" def __repr__(self) -> str: if self.order == 1: diff --git a/polytop/polytop/Dihedrals.py b/polytop/polytop/Dihedrals.py index 8f74d13..608905c 100644 --- a/polytop/polytop/Dihedrals.py +++ b/polytop/polytop/Dihedrals.py @@ -191,7 +191,7 @@ def __init__( raise ValueError(f"Unknown dihedral type: {dihedral_type}") # angles and bonds for GROMOS forcefield atom order - if self.format == "gromos": + if self.format == "gromos" or self.format == "charmm": if self.dihedral_type.is_rotational_constraint or self.dihedral_type.is_rotational_constraint_with_constants: if angle_abc := Angle.from_atoms(atom_a, atom_b, atom_c): angle_abc.dihedrals.add(self) @@ -227,6 +227,9 @@ def from_line(cls, line: str, atoms, format: str = "gromos") -> Dihedral: :type line: str :param atoms: list of all Atoms in the Topology :type atoms: List[Atom] + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: the new Dihedral :rtype: Dihedral """ @@ -236,12 +239,16 @@ def from_line(cls, line: str, atoms, format: str = "gromos") -> Dihedral: atom_c = atoms[int(parts[2]) - 1] atom_d = atoms[int(parts[3]) - 1] dihedral_type = Dihedral_type(int(parts[4])) - phase_angle = float(parts[5]) - force_constant = float(parts[6]) + if format=="charmm": + phase_angle = None + force_constant = None + else: + phase_angle = float(parts[5]) + force_constant = float(parts[6]) constants = [] - if dihedral_type.is_rotational_constraint or dihedral_type.is_periodic_planar_constraint: + if format!="charmm" and (dihedral_type.is_rotational_constraint or dihedral_type.is_periodic_planar_constraint): multiplicity = int(parts[7]) - elif dihedral_type.is_planar_constraint or dihedral_type.is_rotational_constraint_with_constants: + elif dihedral_type.is_planar_constraint or dihedral_type.is_rotational_constraint_with_constants or format=="charmm": multiplicity = None # multiplicity is not required for improper dihedrals else: warnings.warn(f"Unknown dihedral type: {dihedral_type}") @@ -410,7 +417,9 @@ def clone_dihedral_changing(self, from_atom: "Atom", to_atom: "Atom") -> Dihedra return new_dihedral def __str__(self): - if self.dihedral_type.is_rotational_constraint or self.dihedral_type.is_periodic_planar_constraint: + if self.format == "charmm": + return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.atom_d.atom_id:>5} {self.dihedral_type:>5}" + elif self.dihedral_type.is_rotational_constraint or self.dihedral_type.is_periodic_planar_constraint: return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.atom_d.atom_id:>5} {self.dihedral_type:>5} {self.phase_angle:>10.4f} {self.force_constant:.4e} {self.multiplicity:>5}" elif self.dihedral_type.is_planar_constraint: return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.atom_d.atom_id:>5} {self.dihedral_type:>5} {self.phase_angle:>10.4f} {self.force_constant:.4e}" diff --git a/polytop/polytop/Topology.py b/polytop/polytop/Topology.py index b154c06..ea064f5 100644 --- a/polytop/polytop/Topology.py +++ b/polytop/polytop/Topology.py @@ -278,6 +278,9 @@ def from_ITP(cls, file_path: str, preprocess=None, format: str = "gromos") -> To :return: the created Topology object. :rtype: Topology """ + if format not in ["gromos", "charmm", "amber", "opls"]: + raise ValueError("Invalid format! Provide 'gromos', 'charmm', 'amber' or 'opls'\ + - note 'gromos' is default if format string is not provided") with open(file_path, "r") as f: lines = f.readlines() @@ -307,9 +310,9 @@ def from_ITP(cls, file_path: str, preprocess=None, format: str = "gromos") -> To atom.element atoms.append(atom) elif section == "bonds": - Bond.from_line(line, atoms) + Bond.from_line(line, atoms, format=format) elif section == "angles": - Angle.from_line(line, atoms) + Angle.from_line(line, atoms, format=format) elif section == "pairs": Pair.from_line(line, atoms) elif section == "dihedrals": diff --git a/tests/data/CHARMM_pnipam_gmx.itp b/tests/data/CHARMM_pnipam_gmx.itp new file mode 100644 index 0000000..49083dd --- /dev/null +++ b/tests/data/CHARMM_pnipam_gmx.itp @@ -0,0 +1,243 @@ +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 pni rtp pni q +0.0 + 1 OG2D1 1 pni O1 1 -0.514 15.9994 ; qtot -0.514 + 2 NG2S1 1 pni N2 2 -0.481 14.007 ; qtot -0.481 + 3 CG311 1 pni C3 3 -0.005 12.011 ; qtot -0.005 + 4 CG321 1 pni C4 4 -0.216 12.011 ; qtot -0.216 + 5 CG311 1 pni C5 5 0.021 12.011 ; qtot 0.021 + 6 CG2O1 1 pni C6 6 0.54 12.011 ; qtot 0.54 + 7 CG331 1 pni C7 7 -0.272 12.011 ; qtot -0.272 + 8 CG331 1 pni C8 8 -0.298 12.011 ; qtot -0.298 + 9 CG331 1 pni C9 9 -0.269 12.011 ; qtot -0.269 + 10 CG331 1 pni C10 10 -0.269 12.011 ; qtot -0.269 + 11 HGA1 1 pni H11 11 0.09 1.008 ; qtot 0.09 + 12 HGA2 1 pni H12 12 0.09 1.008 ; qtot 0.09 + 13 HGA2 1 pni H13 13 0.09 1.008 ; qtot 0.09 + 14 HGA1 1 pni H14 14 0.09 1.008 ; qtot 0.09 + 15 HGP1 1 pni H15 15 0.323 1.008 ; qtot 0.323 + 16 HGA3 1 pni H16 16 0.09 1.008 ; qtot 0.09 + 17 HGA3 1 pni H17 17 0.09 1.008 ; qtot 0.09 + 18 HGA3 1 pni H18 18 0.09 1.008 ; qtot 0.09 + 19 HGA3 1 pni H19 19 0.09 1.008 ; qtot 0.09 + 20 HGA3 1 pni H20 20 0.09 1.008 ; qtot 0.09 + 21 HGA3 1 pni H21 21 0.09 1.008 ; qtot 0.09 + 22 HGA3 1 pni H22 22 0.09 1.008 ; qtot 0.09 + 23 HGA3 1 pni H23 23 0.09 1.008 ; qtot 0.09 + 24 HGA3 1 pni H24 24 0.09 1.008 ; qtot 0.09 + 25 HGA3 1 pni H25 25 0.09 1.008 ; qtot 0.09 + 26 HGA3 1 pni H26 26 0.09 1.008 ; qtot 0.09 + 27 HGA3 1 pni H27 27 0.09 1.008 ; qtot 0.09 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 1 6 1 + 2 5 1 + 2 6 1 + 2 15 1 + 3 4 1 + 3 6 1 + 3 7 1 + 3 11 1 + 4 8 1 + 4 12 1 + 4 13 1 + 5 9 1 + 5 10 1 + 5 14 1 + 7 16 1 + 7 17 1 + 7 18 1 + 8 19 1 + 8 20 1 + 8 21 1 + 9 22 1 + 9 23 1 + 9 24 1 + 10 25 1 + 10 26 1 + 10 27 1 + +[ pairs ] +; ai aj funct c0 c1 c2 c3 + 1 4 1 + 1 5 1 + 1 7 1 + 1 11 1 + 1 15 1 + 2 4 1 + 2 7 1 + 2 11 1 + 2 22 1 + 2 23 1 + 2 24 1 + 2 25 1 + 2 26 1 + 2 27 1 + 3 5 1 + 3 15 1 + 3 19 1 + 3 20 1 + 3 21 1 + 4 16 1 + 4 17 1 + 4 18 1 + 6 8 1 + 6 9 1 + 6 10 1 + 6 12 1 + 6 13 1 + 6 14 1 + 6 16 1 + 6 17 1 + 6 18 1 + 7 8 1 + 7 12 1 + 7 13 1 + 8 11 1 + 9 15 1 + 9 25 1 + 9 26 1 + 9 27 1 + 10 15 1 + 10 22 1 + 10 23 1 + 10 24 1 + 11 12 1 + 11 13 1 + 11 16 1 + 11 17 1 + 11 18 1 + 12 19 1 + 12 20 1 + 12 21 1 + 13 19 1 + 13 20 1 + 13 21 1 + 14 15 1 + 14 22 1 + 14 23 1 + 14 24 1 + 14 25 1 + 14 26 1 + 14 27 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 5 2 6 5 + 5 2 15 5 + 6 2 15 5 + 4 3 6 5 + 4 3 7 5 + 4 3 11 5 + 6 3 7 5 + 6 3 11 5 + 7 3 11 5 + 3 4 8 5 + 3 4 12 5 + 3 4 13 5 + 8 4 12 5 + 8 4 13 5 + 12 4 13 5 + 2 5 9 5 + 2 5 10 5 + 2 5 14 5 + 9 5 10 5 + 9 5 14 5 + 10 5 14 5 + 1 6 2 5 + 1 6 3 5 + 2 6 3 5 + 3 7 16 5 + 3 7 17 5 + 3 7 18 5 + 16 7 17 5 + 16 7 18 5 + 17 7 18 5 + 4 8 19 5 + 4 8 20 5 + 4 8 21 5 + 19 8 20 5 + 19 8 21 5 + 20 8 21 5 + 5 9 22 5 + 5 9 23 5 + 5 9 24 5 + 22 9 23 5 + 22 9 24 5 + 23 9 24 5 + 5 10 25 5 + 5 10 26 5 + 5 10 27 5 + 25 10 26 5 + 25 10 27 5 + 26 10 27 5 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 6 2 5 9 9 + 6 2 5 10 9 + 6 2 5 14 9 + 15 2 5 9 9 + 15 2 5 10 9 + 15 2 5 14 9 + 5 2 6 1 9 + 5 2 6 3 9 + 15 2 6 1 9 + 15 2 6 3 9 + 6 3 4 8 9 + 6 3 4 12 9 + 6 3 4 13 9 + 7 3 4 8 9 + 7 3 4 12 9 + 7 3 4 13 9 + 11 3 4 8 9 + 11 3 4 12 9 + 11 3 4 13 9 + 4 3 6 1 9 + 4 3 6 2 9 + 7 3 6 1 9 + 7 3 6 2 9 + 11 3 6 1 9 + 11 3 6 2 9 + 4 3 7 16 9 + 4 3 7 17 9 + 4 3 7 18 9 + 6 3 7 16 9 + 6 3 7 17 9 + 6 3 7 18 9 + 11 3 7 16 9 + 11 3 7 17 9 + 11 3 7 18 9 + 3 4 8 19 9 + 3 4 8 20 9 + 3 4 8 21 9 + 12 4 8 19 9 + 12 4 8 20 9 + 12 4 8 21 9 + 13 4 8 19 9 + 13 4 8 20 9 + 13 4 8 21 9 + 2 5 9 22 9 + 2 5 9 23 9 + 2 5 9 24 9 + 10 5 9 22 9 + 10 5 9 23 9 + 10 5 9 24 9 + 14 5 9 22 9 + 14 5 9 23 9 + 14 5 9 24 9 + 2 5 10 25 9 + 2 5 10 26 9 + 2 5 10 27 9 + 9 5 10 25 9 + 9 5 10 26 9 + 9 5 10 27 9 + 14 5 10 25 9 + 14 5 10 26 9 + 14 5 10 27 9 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 6 3 2 1 2 + diff --git a/tests/test_topology.py b/tests/test_topology.py index 4f4632a..4ab0692 100644 --- a/tests/test_topology.py +++ b/tests/test_topology.py @@ -129,6 +129,10 @@ def test_topology_auto_rename_atoms(data_dir: Path, output_dir: Path): assert arg_max_atom_index["N"] == 4 assert arg_max_atom_index["O"] == 2 +def test_topology_bad_format_parser(data_dir: Path, output_dir: Path): + with pytest.raises(ValueError): + check = Topology.from_ITP(data_dir/"OPLS_UNK_460A12.itp", format="pls") + def test_topology_OPLS_parser(data_dir: Path, output_dir: Path): opls = Topology.from_ITP(data_dir/"OPLS_UNK_460A12.itp", format="opls") opls.to_ITP(output_dir/"OPLS_topology.itp", format="opls") @@ -161,6 +165,38 @@ def same_properties(atom_a, atom_b)-> bool: for a in atom.dihedral_neighbours(): assert any(same_properties(a, new_a) for new_a in new_atom.dihedral_neighbours()) +def test_topology_CHARMM_parser(data_dir: Path, output_dir: Path): + charmm = Topology.from_ITP(data_dir/"CHARMM_pnipam_gmx.itp", format="charmm") + charmm.to_ITP(output_dir/"CHARMM_topology.itp", format="charmm") + charmm_new = Topology.from_ITP(output_dir/"CHARMM_topology.itp", format="charmm") + + def same_properties(atom_a, atom_b)-> bool: + if atom_a.atom_type != atom_b.atom_type: + return False + if atom_a.residue_name != atom_b.residue_name: + return False + if atom_a.residue_id != atom_b.residue_id: + return False + if atom_a.partial_charge != atom_b.partial_charge: + return False + if atom_a.mass != atom_b.mass: + return False + return True + + atoms = charmm.atoms + new_atoms = charmm_new.atoms + assert len(atoms) == len(new_atoms) + for i in range(len(atoms)): + atom = atoms[i] + new_atom = new_atoms[i] + assert same_properties(atom, new_atom) + for a in atom.bond_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.bond_neighbours()) + for a in atom.angle_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.angle_neighbours()) + for a in atom.dihedral_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.dihedral_neighbours()) + @pytest.mark.xfail(reason="New method of separating atoms into unique charge groups and renumbering them before saving to ITP is breaking this test.") def test_reverse_topology(data_dir: Path, output_dir: Path): glu = Topology.from_ITP(data_dir/"glutamine.itp") From df78a933706c396fb45bc8ccda05503b7fbfbd03 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Mon, 3 Feb 2025 15:08:45 +1000 Subject: [PATCH 06/12] ITP reader and writer now supportive of AMBER forcefield format. Added a shuffling method and appropriate warning messages to Dihedral initialiser, where the order of atom B and atom C is shuffled and retried if the angles inside the dihedral cannot be resolved. Other changes to Dihedral __str__ representation for the periodic improper dihedral type --- polytop/polytop/Dihedrals.py | 123 ++++++++++++--- polytop/polytop/Topology.py | 27 ++-- tests/data/AMBER_pnipam_GMX.itp | 259 +++++++++++++++++++++++++++++++ tests/data/CHARMM_pnipam_gmx.itp | 3 +- tests/test_topology.py | 36 ++++- 5 files changed, 416 insertions(+), 32 deletions(-) create mode 100644 tests/data/AMBER_pnipam_GMX.itp diff --git a/polytop/polytop/Dihedrals.py b/polytop/polytop/Dihedrals.py index 608905c..d7b1dc6 100644 --- a/polytop/polytop/Dihedrals.py +++ b/polytop/polytop/Dihedrals.py @@ -3,6 +3,8 @@ import warnings from enum import IntEnum from typing import Dict, List, Union +# import pdb +# pdb.set_trace() from .Angles import Angle @@ -190,7 +192,7 @@ def __init__( else: raise ValueError(f"Unknown dihedral type: {dihedral_type}") - # angles and bonds for GROMOS forcefield atom order + # angles and bonds for GROMOS and CHARMM forcefield atom orders if self.format == "gromos" or self.format == "charmm": if self.dihedral_type.is_rotational_constraint or self.dihedral_type.is_rotational_constraint_with_constants: if angle_abc := Angle.from_atoms(atom_a, atom_b, atom_c): @@ -216,6 +218,68 @@ def __init__( raise ValueError(f"Could not find angle for dihedral: {self}") else: raise ValueError(f"Unknown dihedral type: {dihedral_type}") + + # angles and bonds for AMBER forcefield atom order + if self.format == "amber": + if self.dihedral_type.is_periodic_planar_constraint: + if angle_bac := Angle.from_atoms(atom_a, atom_b, atom_c): + angle_bac.dihedrals.add(self) + self.angle_a = angle_bac + else: # could not resolve angles, shuffle and retry + if self.phase_angle == 180 and self.multiplicity == 2: + warnings.warn(f"Could not find angle for dihedral: {self}," + f" swapping the order of atom {self.atom_b.atom_name} and" + f" atom {self.atom_c.atom_name} and retrying. The phase angle" + " is 180 and the multiplicity is 2, so the" + " dihedral parameters will not be impacted.") + if angle_bac := Angle.from_atoms(atom_a, atom_c, atom_b): + angle_bac.dihedrals.add(self) + self.angle_a = angle_bac + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_bad := Angle.from_atoms(atom_a, atom_b, atom_d): + angle_bad.dihedrals.add(self) + self.angle_b = angle_bad + else: # could not resolve angles, shuffle and retry + if self.phase_angle == 180 and self.multiplicity == 2: + warnings.warn(f"Could not find angle for dihedral: {self}," + f" swapping the order of atom {self.atom_b.atom_name} and" + f" atom {self.atom_c.atom_name} and retrying. The phase angle" + " is 180 and the multiplicity is 2, so the" + " dihedral parameters will not be impacted.") + if angle_bad := Angle.from_atoms(atom_a, atom_c, atom_d): + angle_bad.dihedrals.add(self) + self.angle_b = angle_bad + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + elif self.dihedral_type.is_rotational_constraint or self.dihedral_type.is_rotational_constraint_with_constants: + if angle_abc := Angle.from_atoms(atom_a, atom_b, atom_c): + angle_abc.dihedrals.add(self) + self.angle_a = angle_abc + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_bcd := Angle.from_atoms(atom_b, atom_c, atom_d): + angle_bcd.dihedrals.add(self) + self.angle_b = angle_bcd + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + elif self.dihedral_type.is_planar_constraint: + if angle_bac := Angle.from_atoms(atom_a, atom_b, atom_c): + angle_bac.dihedrals.add(self) + self.angle_a = angle_bac + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_bad := Angle.from_atoms(atom_a, atom_b, atom_d): + angle_bad.dihedrals.add(self) + self.angle_b = angle_bad + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + else: + raise ValueError(f"Unknown dihedral type: {dihedral_type}") @classmethod def from_line(cls, line: str, atoms, format: str = "gromos") -> Dihedral: @@ -280,18 +344,11 @@ def find_angles( atom_b: "Atom", atom_c: "Atom", atom_d: "Atom", + format: str = "gromos", ) -> tuple[Angle|None, Angle|None]: """ Class method to find Angles present in this Dihedral. - :param atom_a: The first atom involved in the angle. - :type atom_a: Atom - :param atom_b: The central atom in the angle. - :type atom_b: Atom - :param atom_c: The third atom involved in the angle. - :type atom_c: Atom - - :param atom_a: The first atom involved in the Dihedral. :type atom_a: Atom :param atom_b: The second atom involved in the Dihedral. @@ -300,15 +357,31 @@ def find_angles( :type atom_c: Atom :param atom_d: The fourth atom involved in the Dihedral. :type atom_d: Atom + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: a tuple containing the two Angles involved in this Dihedral :rtype: tuple[Angle, Angle] or tuple[None, None] if dihedral type is neither proper or improper """ - angle_abc = Angle.from_atoms(atom_a, atom_b, atom_c) - angle_bcd = Angle.from_atoms(atom_b, atom_c, atom_d) + if format=="gromos" or format=="charmm": + angle_abc = Angle.from_atoms(atom_a, atom_b, atom_c) + angle_bcd = Angle.from_atoms(atom_b, atom_c, atom_d) + + angle_bac = Angle.from_atoms(atom_b, atom_a, atom_c) + angle_bad = Angle.from_atoms(atom_b, atom_a, atom_d) + elif format == "opls": + angle_abc = Angle.from_atoms(atom_a, atom_b, atom_c) + angle_bcd = Angle.from_atoms(atom_b, atom_c, atom_d) - angle_bac = Angle.from_atoms(atom_b, atom_a, atom_c) - angle_bad = Angle.from_atoms(atom_b, atom_a, atom_d) + angle_bac = Angle.from_atoms(atom_b, atom_a, atom_c) + angle_bad = Angle.from_atoms(atom_a, atom_b, atom_d) + else: # format == "amber" + angle_abc = Angle.from_atoms(atom_a, atom_b, atom_c) + angle_bcd = Angle.from_atoms(atom_b, atom_c, atom_d) + + angle_bac = Angle.from_atoms(atom_b, atom_a, atom_c) + angle_bad = Angle.from_atoms(atom_b, atom_a, atom_d) if ( angle_abc and angle_bcd and angle_abc.dihedrals & angle_bcd.dihedrals @@ -365,6 +438,7 @@ def from_atoms( atom_b: "Atom", atom_c: "Atom", atom_d: "Atom", + format: str = "gromos" ) -> Dihedral: """ Class method to construct Dihedral from four Atoms. There must be at @@ -379,11 +453,14 @@ def from_atoms( :type atom_c: Atom :param atom_d: The fourth atom involved in the Dihedral :type atom_d: Atom + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: the new Dihedral, or None if the Dihedral_type is neither proper or improper :rtype: Dihedral """ - angle_a, angle_b = Dihedral.find_angles(atom_a, atom_b, atom_c, atom_d) + angle_a, angle_b = Dihedral.find_angles(atom_a, atom_b, atom_c, atom_d, format) if angle_a is None or angle_b is None: return None common_dihedrals = angle_a.dihedrals & angle_b.dihedrals @@ -441,7 +518,8 @@ def to_dict(self) -> dict: 'dihedral_type': self.dihedral_type, 'phase_angle': self.phase_angle, 'force_constant': self.force_constant, - 'multiplicity': self.multiplicity} + 'multiplicity': self.multiplicity, + 'constants' = self.constants} :return: a dictionary containing the id's of its Atoms and other attributes of this Dihedral. @@ -456,10 +534,11 @@ def to_dict(self) -> dict: 'phase_angle': self.phase_angle, 'force_constant': self.force_constant, 'multiplicity': self.multiplicity, + 'constants': self.constants, } @classmethod - def from_dict(cls, data: Dict[str, Union[int, float]], atoms: List["Atom"]) -> Dihedral: + def from_dict(cls, data: Dict[str, Union[int, float]], atoms: List["Atom"], format: str = "gromos") -> Dihedral: """ Create a new Dihedral from a dictionary (such as that created with Dihedral.to_dict()) and list of Atoms. Will retrieve an existing @@ -473,7 +552,8 @@ def from_dict(cls, data: Dict[str, Union[int, float]], atoms: List["Atom"]) -> D 'dihedral_type': self.dihedral_type, 'phase_angle': self.phase_angle, 'force_constant': self.force_constant, - 'multiplicity': self.multiplicity} + 'multiplicity': self.multiplicity, + 'constants' = self.constants} :param data: dictionary containing data to make a Dihedral, generate with 'to_dict()'. @@ -482,6 +562,9 @@ def from_dict(cls, data: Dict[str, Union[int, float]], atoms: List["Atom"]) -> D long as the id's of the four atoms specified in the data dict are present. :type atoms: List[Atom] + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: a new Dihedral :rtype: Dihedral """ @@ -490,7 +573,7 @@ def from_dict(cls, data: Dict[str, Union[int, float]], atoms: List["Atom"]) -> D atom_c = next((atom for atom in atoms if atom.atom_id == data['atom_c']), None) atom_d = next((atom for atom in atoms if atom.atom_id == data['atom_d']), None) # check for existing dihedrals - dihedral = Dihedral.from_atoms(atom_a, atom_b, atom_c, atom_d) + dihedral = Dihedral.from_atoms(atom_a, atom_b, atom_c, atom_d, format=format) if dihedral is not None: return dihedral else: @@ -498,5 +581,7 @@ def from_dict(cls, data: Dict[str, Union[int, float]], atoms: List["Atom"]) -> D dihedral_type = data['dihedral_type'], phase_angle = data['phase_angle'], force_constant = data['force_constant'], - multiplicity = data['multiplicity']) + multiplicity = data['multiplicity'], + constants = data['constants'], + format = format) diff --git a/polytop/polytop/Topology.py b/polytop/polytop/Topology.py index ea064f5..003cfee 100644 --- a/polytop/polytop/Topology.py +++ b/polytop/polytop/Topology.py @@ -51,6 +51,7 @@ def __init__( atoms: Optional[List[Atom]] = None, preamble: Optional[List[str]] = None, molecule_type: Optional[MoleculeType] = None, + format: str = "gromos", ): """ Represents the topology of a molecular system, including atoms, bonds, @@ -64,6 +65,9 @@ def __init__( :param molecule_type: the type of molecule represented by the topology, defaults to None :type molecule_type: Optional[MoleculeType], optional + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. """ self.molecule_type = molecule_type self.atoms = atoms or [] @@ -71,6 +75,7 @@ def __init__( self.title = "Unknown molecule" if self.preamble and self.preamble[1].startswith(';'): self.title = self.preamble[1].lstrip('; ') + self.format = format def copy(self) -> Topology: """ @@ -94,11 +99,12 @@ def copy(self) -> Topology: for angle in self.angles: Angle.from_dict(angle.to_dict(),new_atoms) for dihedral in self.dihedrals: - Dihedral.from_dict(dihedral.to_dict(),new_atoms) + Dihedral.from_dict(dihedral.to_dict(),new_atoms,format=self.format) new_topology = Topology( atoms=new_atoms, preamble=self.preamble.copy(), - molecule_type=copy.copy(self.molecule_type) + molecule_type=copy.copy(self.molecule_type), + format=self.format, ) return new_topology @@ -298,6 +304,9 @@ def from_ITP(cls, file_path: str, preprocess=None, format: str = "gromos") -> To continue if line.startswith("["): section = line.strip("[] ").lower() + if section.__contains__(";"): # cleanup and remove comments if present + cut = section.split(";")[0] + section = cut.strip("[] ") continue if preprocess is not None: line = preprocess(section, line) @@ -326,18 +335,15 @@ def from_ITP(cls, file_path: str, preprocess=None, format: str = "gromos") -> To Exclusion.from_line(line, atoms) else: warnings.warn(f"Unknown section {section} in {file_path}") - return cls(atoms, preamble, molecule_type) + return cls(atoms, preamble, molecule_type, format) - def to_ITP(self, file_path: str, format: str = "gromos"): + def to_ITP(self, file_path: str): """ Write the Topology to a GROMACS ITP file of the desired forcefield format. :param file_path: the path to and the desired name of the GROMACS ITP file. :type file_path: str - :param format: The forcefield the ITP file is formatted as, options are - "gromos", "amber", "opls" and "charmm" - :type format: str, defaults to "gromos" for GROMOS forcefields. """ with open(file_path, "w") as f: if self.title: @@ -909,7 +915,7 @@ def to_dict(self) -> dict: } @classmethod - def from_dict(cls, data: dict) -> Topology: + def from_dict(cls, data: dict, format: str = "gromos") -> Topology: """ Create a new Topology from a dictionary, such as that created with Topology.to_dict(). @@ -927,6 +933,9 @@ def from_dict(cls, data: dict) -> Topology: :param data: dictionary containing data to make a Topology, generate with 'to_dict()'. :type data: dict + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: a new Topology :rtype: Topology """ @@ -943,7 +952,7 @@ def from_dict(cls, data: dict) -> Topology: Angle.from_dict(angle_data,topology.atoms) for dihedral_data in data["dihedrals"]: - Dihedral.from_dict(dihedral_data,topology.atoms) + Dihedral.from_dict(dihedral_data,topology.atoms, format=format) for pair_data in data["pairs"]: Pair.from_dict(pair_data,topology.atoms) diff --git a/tests/data/AMBER_pnipam_GMX.itp b/tests/data/AMBER_pnipam_GMX.itp new file mode 100644 index 0000000..35dda60 --- /dev/null +++ b/tests/data/AMBER_pnipam_GMX.itp @@ -0,0 +1,259 @@ +[ atoms ] +; nr type resi res atom cgnr charge mass ; qtot bond_type + 1 o 1 UNL O 1 -0.612100 16.00000 ; qtot -0.612 + 2 ns 1 UNL N 2 -0.575900 14.01000 ; qtot -1.188 + 3 c3 1 UNL C 3 -0.131700 12.01000 ; qtot -1.320 + 4 c3 1 UNL C1 4 -0.072400 12.01000 ; qtot -1.392 + 5 c3 1 UNL C2 5 0.096700 12.01000 ; qtot -1.295 + 6 c 1 UNL C3 6 0.664102 12.01000 ; qtot -0.631 + 7 c3 1 UNL C4 7 -0.092100 12.01000 ; qtot -0.723 + 8 c3 1 UNL C5 8 -0.096100 12.01000 ; qtot -0.819 + 9 c3 1 UNL C6 9 -0.110100 12.01000 ; qtot -0.930 + 10 c3 1 UNL C7 10 -0.110100 12.01000 ; qtot -1.040 + 11 hc 1 UNL H 11 0.057700 1.00800 ; qtot -0.982 + 12 hc 1 UNL H1 12 0.054700 1.00800 ; qtot -0.927 + 13 hc 1 UNL H2 13 0.054700 1.00800 ; qtot -0.873 + 14 h1 1 UNL H3 14 0.089700 1.00800 ; qtot -0.783 + 15 hn 1 UNL H4 15 0.304500 1.00800 ; qtot -0.478 + 16 hc 1 UNL H5 16 0.043033 1.00800 ; qtot -0.435 + 17 hc 1 UNL H6 17 0.043033 1.00800 ; qtot -0.392 + 18 hc 1 UNL H7 18 0.043033 1.00800 ; qtot -0.349 + 19 hc 1 UNL H8 19 0.037033 1.00800 ; qtot -0.312 + 20 hc 1 UNL H9 20 0.037033 1.00800 ; qtot -0.275 + 21 hc 1 UNL H10 21 0.037033 1.00800 ; qtot -0.238 + 22 hc 1 UNL H11 22 0.039700 1.00800 ; qtot -0.199 + 23 hc 1 UNL H12 23 0.039700 1.00800 ; qtot -0.159 + 24 hc 1 UNL H13 24 0.039700 1.00800 ; qtot -0.119 + 25 hc 1 UNL H14 25 0.039700 1.00800 ; qtot -0.079 + 26 hc 1 UNL H15 26 0.039700 1.00800 ; qtot -0.040 + 27 hc 1 UNL H16 27 0.039700 1.00800 ; qtot -0.000 + +[ bonds ] +; ai aj funct r k + 1 6 1 1.2180e-01 5.4610e+05 ; O - C3 + 2 5 1 1.4620e-01 2.2075e+05 ; N - C2 + 2 6 1 1.3790e-01 2.9807e+05 ; N - C3 + 2 15 1 1.0130e-01 4.4124e+05 ; N - H4 + 3 4 1 1.5380e-01 1.9456e+05 ; C - C1 + 3 6 1 1.5240e-01 2.0351e+05 ; C - C3 + 3 7 1 1.5380e-01 1.9456e+05 ; C - C4 + 3 11 1 1.0970e-01 3.1455e+05 ; C - H + 4 8 1 1.5380e-01 1.9456e+05 ; C1 - C5 + 4 12 1 1.0970e-01 3.1455e+05 ; C1 - H1 + 4 13 1 1.0970e-01 3.1455e+05 ; C1 - H2 + 5 9 1 1.5380e-01 1.9456e+05 ; C2 - C6 + 5 10 1 1.5380e-01 1.9456e+05 ; C2 - C7 + 5 14 1 1.0970e-01 3.1455e+05 ; C2 - H3 + 7 16 1 1.0970e-01 3.1455e+05 ; C4 - H5 + 7 17 1 1.0970e-01 3.1455e+05 ; C4 - H6 + 7 18 1 1.0970e-01 3.1455e+05 ; C4 - H7 + 8 19 1 1.0970e-01 3.1455e+05 ; C5 - H8 + 8 20 1 1.0970e-01 3.1455e+05 ; C5 - H9 + 8 21 1 1.0970e-01 3.1455e+05 ; C5 - H10 + 9 22 1 1.0970e-01 3.1455e+05 ; C6 - H11 + 9 23 1 1.0970e-01 3.1455e+05 ; C6 - H12 + 9 24 1 1.0970e-01 3.1455e+05 ; C6 - H13 + 10 25 1 1.0970e-01 3.1455e+05 ; C7 - H14 + 10 26 1 1.0970e-01 3.1455e+05 ; C7 - H15 + 10 27 1 1.0970e-01 3.1455e+05 ; C7 - H16 + +[ pairs ] +; ai aj funct + 1 4 1 ; O - C1 + 1 5 1 ; O - C2 + 1 7 1 ; O - C4 + 1 11 1 ; O - H + 1 15 1 ; O - H4 + 2 4 1 ; N - C1 + 2 7 1 ; N - C4 + 2 11 1 ; N - H + 2 22 1 ; N - H11 + 2 23 1 ; N - H12 + 2 24 1 ; N - H13 + 2 25 1 ; N - H14 + 2 26 1 ; N - H15 + 2 27 1 ; N - H16 + 3 5 1 ; C - C2 + 3 15 1 ; C - H4 + 3 19 1 ; C - H8 + 3 20 1 ; C - H9 + 3 21 1 ; C - H10 + 4 16 1 ; C1 - H5 + 4 17 1 ; C1 - H6 + 4 18 1 ; C1 - H7 + 6 8 1 ; C3 - C5 + 6 9 1 ; C3 - C6 + 6 10 1 ; C3 - C7 + 6 12 1 ; C3 - H1 + 6 13 1 ; C3 - H2 + 6 14 1 ; C3 - H3 + 6 16 1 ; C3 - H5 + 6 17 1 ; C3 - H6 + 6 18 1 ; C3 - H7 + 7 8 1 ; C4 - C5 + 7 12 1 ; C4 - H1 + 7 13 1 ; C4 - H2 + 8 11 1 ; C5 - H + 9 15 1 ; C6 - H4 + 9 25 1 ; C6 - H14 + 9 26 1 ; C6 - H15 + 9 27 1 ; C6 - H16 + 10 15 1 ; C7 - H4 + 10 22 1 ; C7 - H11 + 10 23 1 ; C7 - H12 + 10 24 1 ; C7 - H13 + 11 12 1 ; H - H1 + 11 13 1 ; H - H2 + 11 16 1 ; H - H5 + 11 17 1 ; H - H6 + 11 18 1 ; H - H7 + 12 19 1 ; H1 - H8 + 12 20 1 ; H1 - H9 + 12 21 1 ; H1 - H10 + 13 19 1 ; H2 - H8 + 13 20 1 ; H2 - H9 + 13 21 1 ; H2 - H10 + 14 15 1 ; H3 - H4 + 14 22 1 ; H3 - H11 + 14 23 1 ; H3 - H12 + 14 24 1 ; H3 - H13 + 14 25 1 ; H3 - H14 + 14 26 1 ; H3 - H15 + 14 27 1 ; H3 - H16 + +[ angles ] +; ai aj ak funct theta cth + 1 6 2 1 1.2305e+02 9.5228e+02 ; O - C3 - N + 1 6 3 1 1.2320e+02 7.0793e+02 ; O - C3 - C + 2 5 9 1 1.1161e+02 6.9622e+02 ; N - C2 - C6 + 2 5 10 1 1.1161e+02 6.9622e+02 ; N - C2 - C7 + 2 5 14 1 1.0888e+02 5.1463e+02 ; N - C2 - H3 + 2 6 3 1 1.1518e+02 7.0542e+02 ; N - C3 - C + 3 4 8 1 1.1151e+02 5.4308e+02 ; C - C1 - C5 + 3 4 12 1 1.0980e+02 3.9162e+02 ; C - C1 - H1 + 3 4 13 1 1.0980e+02 3.9162e+02 ; C - C1 - H2 + 3 7 16 1 1.0980e+02 3.9162e+02 ; C - C4 - H5 + 3 7 17 1 1.0980e+02 3.9162e+02 ; C - C4 - H6 + 3 7 18 1 1.0980e+02 3.9162e+02 ; C - C4 - H7 + 4 3 6 1 1.1104e+02 5.4643e+02 ; C1 - C - C3 + 4 3 7 1 1.1151e+02 5.4308e+02 ; C1 - C - C4 + 4 3 11 1 1.0980e+02 3.9162e+02 ; C1 - C - H + 4 8 19 1 1.0980e+02 3.9162e+02 ; C1 - C5 - H8 + 4 8 20 1 1.0980e+02 3.9162e+02 ; C1 - C5 - H9 + 4 8 21 1 1.0980e+02 3.9162e+02 ; C1 - C5 - H10 + 5 2 6 1 1.2069e+02 5.4643e+02 ; C2 - N - C3 + 5 2 15 1 1.1768e+02 3.8576e+02 ; C2 - N - H4 + 5 9 22 1 1.0980e+02 3.9162e+02 ; C2 - C6 - H11 + 5 9 23 1 1.0980e+02 3.9162e+02 ; C2 - C6 - H12 + 5 9 24 1 1.0980e+02 3.9162e+02 ; C2 - C6 - H13 + 5 10 25 1 1.0980e+02 3.9162e+02 ; C2 - C7 - H14 + 5 10 26 1 1.0980e+02 3.9162e+02 ; C2 - C7 - H15 + 5 10 27 1 1.0980e+02 3.9162e+02 ; C2 - C7 - H16 + 6 2 15 1 1.1755e+02 4.0752e+02 ; C3 - N - H4 + 6 3 7 1 1.1104e+02 5.4643e+02 ; C3 - C - C4 + 6 3 11 1 1.0877e+02 3.9664e+02 ; C3 - C - H + 7 3 11 1 1.0980e+02 3.9162e+02 ; C4 - C - H + 8 4 12 1 1.0980e+02 3.9162e+02 ; C5 - C1 - H1 + 8 4 13 1 1.0980e+02 3.9162e+02 ; C5 - C1 - H2 + 9 5 10 1 1.1151e+02 5.4308e+02 ; C6 - C2 - C7 + 9 5 14 1 1.0956e+02 3.9246e+02 ; C6 - C2 - H3 + 10 5 14 1 1.0956e+02 3.9246e+02 ; C7 - C2 - H3 + 12 4 13 1 1.0758e+02 3.2635e+02 ; H1 - C1 - H2 + 16 7 17 1 1.0758e+02 3.2635e+02 ; H5 - C4 - H6 + 16 7 18 1 1.0758e+02 3.2635e+02 ; H5 - C4 - H7 + 17 7 18 1 1.0758e+02 3.2635e+02 ; H6 - C4 - H7 + 19 8 20 1 1.0758e+02 3.2635e+02 ; H8 - C5 - H9 + 19 8 21 1 1.0758e+02 3.2635e+02 ; H8 - C5 - H10 + 20 8 21 1 1.0758e+02 3.2635e+02 ; H9 - C5 - H10 + 22 9 23 1 1.0758e+02 3.2635e+02 ; H11 - C6 - H12 + 22 9 24 1 1.0758e+02 3.2635e+02 ; H11 - C6 - H13 + 23 9 24 1 1.0758e+02 3.2635e+02 ; H12 - C6 - H13 + 25 10 26 1 1.0758e+02 3.2635e+02 ; H14 - C7 - H15 + 25 10 27 1 1.0758e+02 3.2635e+02 ; H14 - C7 - H16 + 26 10 27 1 1.0758e+02 3.2635e+02 ; H15 - C7 - H16 + +[ dihedrals ] ; propers +; for gromacs 4.5 or higher, using funct 9 +; i j k l func phase kd pn + 1 6 2 5 9 180.00 10.46000 2 ; O- C3- N- C2 + 1 6 2 15 9 0.00 8.36800 1 ; O- C3- N- H4 + 1 6 2 15 9 180.00 10.46000 2 ; O- C3- N- H4 + 1 6 3 4 9 0.00 3.09616 1 ; O- C3- C- C1 + 1 6 3 4 9 180.00 1.12968 2 ; O- C3- C- C1 + 1 6 3 4 9 180.00 2.30120 3 ; O- C3- C- C1 + 1 6 3 7 9 0.00 3.09616 1 ; O- C3- C- C4 + 1 6 3 7 9 180.00 1.12968 2 ; O- C3- C- C4 + 1 6 3 7 9 180.00 2.30120 3 ; O- C3- C- C4 + 1 6 3 11 9 0.00 3.47272 1 ; O- C3- C- H + 1 6 3 11 9 180.00 0.16736 3 ; O- C3- C- H + 2 5 9 22 9 0.00 0.65084 3 ; N- C2- C6- H11 + 2 5 9 23 9 0.00 0.65084 3 ; N- C2- C6- H12 + 2 5 9 24 9 0.00 0.65084 3 ; N- C2- C6- H13 + 2 5 10 25 9 0.00 0.65084 3 ; N- C2- C7- H14 + 2 5 10 26 9 0.00 0.65084 3 ; N- C2- C7- H15 + 2 5 10 27 9 0.00 0.65084 3 ; N- C2- C7- H16 + 2 6 3 4 9 180.00 0.00000 4 ; N- C3- C- C1 + 2 6 3 4 9 180.00 2.97064 2 ; N- C3- C- C1 + 2 6 3 7 9 180.00 0.00000 4 ; N- C3- C- C4 + 2 6 3 7 9 180.00 2.97064 2 ; N- C3- C- C4 + 2 6 3 11 9 180.00 0.00000 2 ; N- C3- C- H + 3 4 8 19 9 0.00 0.33472 3 ; C- C1- C5- H8 + 3 4 8 20 9 0.00 0.33472 3 ; C- C1- C5- H9 + 3 4 8 21 9 0.00 0.33472 3 ; C- C1- C5- H10 + 3 6 2 5 9 0.00 2.09200 1 ; C- C3- N- C2 + 3 6 2 5 9 180.00 1.08784 2 ; C- C3- N- C2 + 3 6 2 15 9 180.00 10.46000 2 ; C- C3- N- H4 + 4 3 7 16 9 0.00 0.33472 3 ; C1- C- C4- H5 + 4 3 7 17 9 0.00 0.33472 3 ; C1- C- C4- H6 + 4 3 7 18 9 0.00 0.33472 3 ; C1- C- C4- H7 + 6 2 5 9 9 0.00 0.71128 3 ; C3- N- C2- C6 + 6 2 5 9 9 180.00 0.41840 4 ; C3- N- C2- C6 + 6 2 5 9 9 180.00 4.26768 1 ; C3- N- C2- C6 + 6 2 5 10 9 0.00 0.71128 3 ; C3- N- C2- C7 + 6 2 5 10 9 180.00 0.41840 4 ; C3- N- C2- C7 + 6 2 5 10 9 180.00 4.26768 1 ; C3- N- C2- C7 + 6 2 5 14 9 180.00 0.00000 2 ; C3- N- C2- H3 + 6 3 4 8 9 0.00 0.41840 3 ; C3- C- C1- C5 + 6 3 4 12 9 0.00 0.65084 3 ; C3- C- C1- H1 + 6 3 4 13 9 0.00 0.65084 3 ; C3- C- C1- H2 + 6 3 7 16 9 0.00 0.65084 3 ; C3- C- C4- H5 + 6 3 7 17 9 0.00 0.65084 3 ; C3- C- C4- H6 + 6 3 7 18 9 0.00 0.65084 3 ; C3- C- C4- H7 + 7 3 4 8 9 0.00 0.46024 1 ; C4- C- C1- C5 + 7 3 4 8 9 0.00 0.54392 3 ; C4- C- C1- C5 + 7 3 4 8 9 180.00 1.21336 2 ; C4- C- C1- C5 + 7 3 4 12 9 0.00 0.33472 3 ; C4- C- C1- H1 + 7 3 4 13 9 0.00 0.33472 3 ; C4- C- C1- H2 + 8 4 3 11 9 0.00 0.33472 3 ; C5- C1- C- H + 9 5 2 15 9 0.00 0.00000 0 ; C6- C2- N- H4 + 9 5 10 25 9 0.00 0.33472 3 ; C6- C2- C7- H14 + 9 5 10 26 9 0.00 0.33472 3 ; C6- C2- C7- H15 + 9 5 10 27 9 0.00 0.33472 3 ; C6- C2- C7- H16 + 10 5 2 15 9 0.00 0.00000 0 ; C7- C2- N- H4 + 10 5 9 22 9 0.00 0.33472 3 ; C7- C2- C6- H11 + 10 5 9 23 9 0.00 0.33472 3 ; C7- C2- C6- H12 + 10 5 9 24 9 0.00 0.33472 3 ; C7- C2- C6- H13 + 11 3 4 12 9 0.00 0.50208 3 ; H- C- C1- H1 + 11 3 4 13 9 0.00 0.50208 3 ; H- C- C1- H2 + 11 3 7 16 9 0.00 0.50208 3 ; H- C- C4- H5 + 11 3 7 17 9 0.00 0.50208 3 ; H- C- C4- H6 + 11 3 7 18 9 0.00 0.50208 3 ; H- C- C4- H7 + 12 4 8 19 9 0.00 0.50208 3 ; H1- C1- C5- H8 + 12 4 8 20 9 0.00 0.50208 3 ; H1- C1- C5- H9 + 12 4 8 21 9 0.00 0.50208 3 ; H1- C1- C5- H10 + 13 4 8 19 9 0.00 0.50208 3 ; H2- C1- C5- H8 + 13 4 8 20 9 0.00 0.50208 3 ; H2- C1- C5- H9 + 13 4 8 21 9 0.00 0.50208 3 ; H2- C1- C5- H10 + 14 5 2 15 9 0.00 0.00000 0 ; H3- C2- N- H4 + 14 5 9 22 9 0.00 0.65084 3 ; H3- C2- C6- H11 + 14 5 9 23 9 0.00 0.65084 3 ; H3- C2- C6- H12 + 14 5 9 24 9 0.00 0.65084 3 ; H3- C2- C6- H13 + 14 5 10 25 9 0.00 0.65084 3 ; H3- C2- C7- H14 + 14 5 10 26 9 0.00 0.65084 3 ; H3- C2- C7- H15 + 14 5 10 27 9 0.00 0.65084 3 ; H3- C2- C7- H16 + +[ dihedrals ] ; impropers +; treated as propers in GROMACS to use correct AMBER analytical function +; i j k l func phase kd pn + 1 6 2 3 4 180.00 43.93200 2 ; O- C3- N- C + 6 5 2 15 4 180.00 4.60240 2 ; C3- C2- N- H4 diff --git a/tests/data/CHARMM_pnipam_gmx.itp b/tests/data/CHARMM_pnipam_gmx.itp index 49083dd..ca3fb0d 100644 --- a/tests/data/CHARMM_pnipam_gmx.itp +++ b/tests/data/CHARMM_pnipam_gmx.itp @@ -239,5 +239,4 @@ [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 - 6 3 2 1 2 - + 6 3 2 1 2 \ No newline at end of file diff --git a/tests/test_topology.py b/tests/test_topology.py index 4ab0692..0ac94c2 100644 --- a/tests/test_topology.py +++ b/tests/test_topology.py @@ -135,7 +135,7 @@ def test_topology_bad_format_parser(data_dir: Path, output_dir: Path): def test_topology_OPLS_parser(data_dir: Path, output_dir: Path): opls = Topology.from_ITP(data_dir/"OPLS_UNK_460A12.itp", format="opls") - opls.to_ITP(output_dir/"OPLS_topology.itp", format="opls") + opls.to_ITP(output_dir/"OPLS_topology.itp") opls_new = Topology.from_ITP(output_dir/"OPLS_topology.itp", format="opls") def same_properties(atom_a, atom_b)-> bool: @@ -167,7 +167,7 @@ def same_properties(atom_a, atom_b)-> bool: def test_topology_CHARMM_parser(data_dir: Path, output_dir: Path): charmm = Topology.from_ITP(data_dir/"CHARMM_pnipam_gmx.itp", format="charmm") - charmm.to_ITP(output_dir/"CHARMM_topology.itp", format="charmm") + charmm.to_ITP(output_dir/"CHARMM_topology.itp") charmm_new = Topology.from_ITP(output_dir/"CHARMM_topology.itp", format="charmm") def same_properties(atom_a, atom_b)-> bool: @@ -197,6 +197,38 @@ def same_properties(atom_a, atom_b)-> bool: for a in atom.dihedral_neighbours(): assert any(same_properties(a, new_a) for new_a in new_atom.dihedral_neighbours()) +def test_topology_AMBER_parser(data_dir: Path, output_dir: Path): + amber = Topology.from_ITP(data_dir/"AMBER_pnipam_GMX.itp", format="amber") + amber.to_ITP(output_dir/"AMBER_topology.itp") + amber_new = Topology.from_ITP(output_dir/"AMBER_topology.itp", format="amber") + + def same_properties(atom_a, atom_b)-> bool: + if atom_a.atom_type != atom_b.atom_type: + return False + if atom_a.residue_name != atom_b.residue_name: + return False + if atom_a.residue_id != atom_b.residue_id: + return False + if atom_a.partial_charge != atom_b.partial_charge: + return False + if atom_a.mass != atom_b.mass: + return False + return True + + atoms = amber.atoms + new_atoms = amber_new.atoms + assert len(atoms) == len(new_atoms) + for i in range(len(atoms)): + atom = atoms[i] + new_atom = new_atoms[i] + assert same_properties(atom, new_atom) + for a in atom.bond_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.bond_neighbours()) + for a in atom.angle_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.angle_neighbours()) + for a in atom.dihedral_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.dihedral_neighbours()) + @pytest.mark.xfail(reason="New method of separating atoms into unique charge groups and renumbering them before saving to ITP is breaking this test.") def test_reverse_topology(data_dir: Path, output_dir: Path): glu = Topology.from_ITP(data_dir/"glutamine.itp") From 330f4f3d8053f0f875d7d3858c33cd2306224477 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Wed, 5 Feb 2025 12:27:35 +1000 Subject: [PATCH 07/12] Large commit message below: Extending support for other forcefield itp files uncovered a bug where undefined, random failure to resolve a dihedral containing the new bond was observed during polymer extension. The cause of this bug was due to the Bond.from_atoms static method, which would find all bonds between a pair of atoms, and if there was more than 1 (in the case of a duplicated bond between two joining atoms during extension) it would return the second bond. This method is envoked to find bonds which will be assigned angles (and thus dihedrals) when a leaving 'residue' atom is replaced by a new 'monomer' atom. As a result, duplicate bonds were found to share half of the angles each, which caused issues when attempting to resolve dihedrals. This was corrected by ensuring the method returns the bond with angles associated if there are duplicates. However, after polymer extension is complete, the bonds are 'deduplicated' to remove a duplicate, and the duplicate that is removed would be the second one iterated through in Atom 'deduplicate_bonds()' -> thus if the second of the two bonds was the one with the angles it would be lost and also result in issues resolving dihedrals in the next polymer extension step. I believe this bug only surfaced now as the test case I was using had a two-atom repeating backbone, so the angles of the bond created in the previous extension step were needed to resolve the dihedrals in the current extension step. I suspect it may also be attributed to changes in dihedral ordering from introducing support to other forcefields, but I am not sure. Changes made: deduplicate_bonds() uses Bond.from_atoms() to select the correct, 'empty' bond to delete Bond.from_atoms() has an optional argument used to specify if it should return the empty bond or the bond with angles, returns the bond with angles by default --- polytop/polytop/Angles.py | 7 +++--- polytop/polytop/Atoms.py | 4 ++- polytop/polytop/Bonds.py | 49 ++++++++++++++++++++---------------- polytop/polytop/Dihedrals.py | 2 +- polytop/polytop/Topology.py | 2 +- 5 files changed, 36 insertions(+), 28 deletions(-) diff --git a/polytop/polytop/Angles.py b/polytop/polytop/Angles.py index 75e1c3e..1a537f9 100644 --- a/polytop/polytop/Angles.py +++ b/polytop/polytop/Angles.py @@ -60,6 +60,7 @@ def __init__(self, atom_a: Atom, atom_b: Atom, atom_c: Atom, self.bond_ab, self.bond_bc = Angle.find_bonds(atom_a, atom_b, atom_c) if self.bond_ab is None or self.bond_bc is None: raise ValueError(f"Could not find bonds for angle: {self}") + self.bond_ab.angles.add(self) self.bond_bc.angles.add(self) self.dihedrals = set() @@ -134,11 +135,11 @@ def clone_angle_changing(self, from_atom: Atom, to_atom: Atom) -> Angle: :rtype: Angle """ if self.atom_a == from_atom: # first atom is being replaced - new_angle = Angle(to_atom, self.atom_b, self.atom_c, self.angle_type, self.angle_value, self.force_constant) + new_angle = Angle(to_atom, self.atom_b, self.atom_c, self.angle_type, self.angle_value, self.force_constant, self.format) elif self.atom_b == from_atom: # second atom is being replaced - new_angle = Angle(self.atom_a, to_atom, self.atom_c, self.angle_type, self.angle_value, self.force_constant) + new_angle = Angle(self.atom_a, to_atom, self.atom_c, self.angle_type, self.angle_value, self.force_constant, self.format) elif self.atom_c == from_atom: # third atom is being replaced - new_angle = Angle(self.atom_a, self.atom_b, to_atom, self.angle_type, self.angle_value, self.force_constant) + new_angle = Angle(self.atom_a, self.atom_b, to_atom, self.angle_type, self.angle_value, self.force_constant, self.format) else: raise ValueError(f"Atom {from_atom} is not in angle {self}") return new_angle diff --git a/polytop/polytop/Atoms.py b/polytop/polytop/Atoms.py index 7e9c066..d643467 100644 --- a/polytop/polytop/Atoms.py +++ b/polytop/polytop/Atoms.py @@ -266,7 +266,9 @@ def deduplicate_bonds(self): bonds_to_remove = [] for bond in self.bonds: if bond.other_atom(self) in neighbours: - bonds_to_remove.append(bond) + # find duplicate bond and add the one without angles to bonds_to_remove + empty_bond = Bond.from_atoms(self, bond.other_atom(self), find_empty = True) + bonds_to_remove.append(empty_bond) else: neighbours.append(bond.other_atom(self)) for bond in bonds_to_remove: diff --git a/polytop/polytop/Bonds.py b/polytop/polytop/Bonds.py index d03b0b3..438a115 100644 --- a/polytop/polytop/Bonds.py +++ b/polytop/polytop/Bonds.py @@ -95,37 +95,42 @@ def from_line(cls, line: str, atoms: List["Atom"], format: str = "gromos") -> Bo return cls(atom_a, atom_b, bond_type, bond_length, force_constant, format=format) @staticmethod - def from_atoms(atom_a: "Atom", atom_b: "Atom") -> Bond: + def from_atoms(atom_a: "Atom", atom_b: "Atom", find_empty: bool = False) -> Bond: """ Class method to find and return Bond from between two Atoms. :param atom_a: The first atom involved in the angle. :type atom_a: Atom - :param atom_b: The central atom in the angle. - :type atom_b: Atom - :param atom_c: The third atom involved in the angle. - :type atom_c: Atom - :return: the new Angle - :rtype: Angle - - :param atom_a: The first atom involved in the bond. - :type atom_a: Atom - :param atom_b: The second atom involved in the bond. + :param atom_b: The second atom in the angle. :type atom_b: Atom + :param find_empty: Optional argument used when de-duplicating bonds to + ensure the bond without angles associated is returned to delete. + :type find_empty: bool, defaults to False :return: a Bond between these Atoms, or None if either atom_a or atom_b are None or there is not a bond between them. :rtype: Bond """ if atom_a is None or atom_b is None: return None - return next( - ( - bond - for bond in atom_a.bonds - if bond.atom_b == atom_b or bond.atom_a == atom_b - ), - None, - ) + + send = list(bond for bond in atom_a.bonds if bond.atom_b == atom_b or bond.atom_a == atom_b) + # need to prevent ambiguity in selecting bonds, so that only one duplicate + # bond created during polymer extension gets all of the Angles and Dihedrals, + # and the other is removed during bond de-duplication + if len(send) > 1 and find_empty==False: + # duplicate bond, return the bond that has angles already to give it more + has_angles = list(bond for bond in send if len(bond.angles)>=1 and bond.angles!=None and bond.angles!=set())[0] + return has_angles + elif len(send) > 1 and find_empty==True: + # duplicate bond, return the bond with no angles to delete + no_angles = list(bond for bond in send if len(bond.angles)==0 or bond.angles==None or bond.angles==set())[0] + return no_angles + elif len(send)==1: + # only 1 bond for this atom pair, return it + return send[0] + else: + # this atom pair does not have a shared bond + return None def contains_atom(self, atom: "Atom") -> bool: """ @@ -154,14 +159,14 @@ def clone_bond_changing(self, from_atom: "Atom", to_atom: "Atom") -> Bond: :rtype: Bond """ if self.atom_a == from_atom: # first atom is being replaced - new_bond = Bond(to_atom, self.atom_b, self.bond_type, self.bond_length, self.force_constant, self.order) + new_bond = Bond(to_atom, self.atom_b, self.bond_type, self.bond_length, self.force_constant, self.order, self.format) elif self.atom_b == from_atom: # second atom is being replaced - new_bond = Bond(self.atom_a, to_atom, self.bond_type, self.bond_length, self.force_constant, self.order) + new_bond = Bond(self.atom_a, to_atom, self.bond_type, self.bond_length, self.force_constant, self.order, self.format) else: raise ValueError(f"Atom {from_atom} is not in bond {self}") return new_bond - def other_atom(self, atom: "Atom")-> Atom: + def other_atom(self, atom: "Atom")-> "Atom": """ Check if the given Atom is in this Angle and return a list of the other atoms present in this Angle (i.e. discluding 'atom'). diff --git a/polytop/polytop/Dihedrals.py b/polytop/polytop/Dihedrals.py index d7b1dc6..1acafc9 100644 --- a/polytop/polytop/Dihedrals.py +++ b/polytop/polytop/Dihedrals.py @@ -374,7 +374,7 @@ def find_angles( angle_abc = Angle.from_atoms(atom_a, atom_b, atom_c) angle_bcd = Angle.from_atoms(atom_b, atom_c, atom_d) - angle_bac = Angle.from_atoms(atom_b, atom_a, atom_c) + angle_bac = Angle.from_atoms(atom_a, atom_b, atom_c) angle_bad = Angle.from_atoms(atom_a, atom_b, atom_d) else: # format == "amber" angle_abc = Angle.from_atoms(atom_a, atom_b, atom_c) diff --git a/polytop/polytop/Topology.py b/polytop/polytop/Topology.py index 003cfee..0b99669 100644 --- a/polytop/polytop/Topology.py +++ b/polytop/polytop/Topology.py @@ -1068,7 +1068,7 @@ def change_atom(self, old_atom: Atom, new_atom: Atom): # change all the bonds for bond in old_atom.bonds: bond.clone_bond_changing(old_atom, new_atom) - + # change all the angles for bond in old_atom.bonds: for angle in bond.angles: From f1652667c409110f1b1762faa170b4fa200d691d Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Wed, 5 Feb 2025 13:59:25 +1000 Subject: [PATCH 08/12] Update paper_worked_example.ipynb output files - no observable/major changes apparent in the output after large bug fix --- data_paper_examples/ethylamine_dendrimer.itp | 1252 ++++++++--------- data_paper_examples/ethylamine_dendrimer.json | 2 +- data_paper_examples/ethylamine_dendrimer.png | Bin 22673 -> 22654 bytes .../four_arm_star_overlapped_monomers.itp | 342 ++--- .../four_arm_star_overlapped_monomers.json | 2 +- .../four_arm_star_overlapped_monomers.png | Bin 16291 -> 16291 bytes data_paper_examples/pei_linear_polymer.itp | 108 +- data_paper_examples/pei_linear_polymer.json | 2 +- data_paper_examples/polyester.itp | 330 ++--- data_paper_examples/polyester.png | Bin 12888 -> 12883 bytes .../six_arm_star_monomer_build.itp | 612 ++++---- .../six_arm_star_monomer_build.json | 2 +- .../six_arm_star_monomer_build.png | Bin 17360 -> 17408 bytes 13 files changed, 1326 insertions(+), 1326 deletions(-) diff --git a/data_paper_examples/ethylamine_dendrimer.itp b/data_paper_examples/ethylamine_dendrimer.itp index 587761c..1865814 100644 --- a/data_paper_examples/ethylamine_dendrimer.itp +++ b/data_paper_examples/ethylamine_dendrimer.itp @@ -95,55 +95,55 @@ 27 HC 4 BB6C H11 27 0.060280 1.0080 28 HC 4 BB6C H12 28 0.060280 1.0080 29 NTer 4 BB6C N1 29 -0.590720 14.0067 - 30 CPos 5 BB6C C6 30 -0.137175 12.0110 - 31 HC 5 BB6C H13 31 0.116825 1.0080 - 32 HC 5 BB6C H14 32 0.116825 1.0080 - 33 CPos 5 BB6C C5 33 0.142825 12.0110 - 34 HC 5 BB6C H11 34 0.060825 1.0080 - 35 HC 5 BB6C H12 35 0.060825 1.0080 - 36 NTer 5 BB6C N1 36 -0.590175 14.0067 - 37 CPos 6 BB6C C6 37 -0.136771 12.0110 - 38 HC 6 BB6C H13 38 0.117229 1.0080 - 39 HC 6 BB6C H14 39 0.117229 1.0080 - 40 CPos 6 BB6C C5 40 0.143229 12.0110 - 41 HC 6 BB6C H11 41 0.061229 1.0080 - 42 HC 6 BB6C H12 42 0.061229 1.0080 - 43 NTer 6 BB6C N1 43 -0.589771 14.0067 - 44 CPos 7 BB6C C6 44 -0.136861 12.0110 - 45 HC 7 BB6C H13 45 0.117139 1.0080 - 46 HC 7 BB6C H14 46 0.117139 1.0080 - 47 CPos 7 BB6C C5 47 0.143139 12.0110 - 48 HC 7 BB6C H11 48 0.061139 1.0080 - 49 HC 7 BB6C H12 49 0.061139 1.0080 - 50 NTer 7 BB6C N1 50 -0.589861 14.0067 - 51 CPos 8 BB6C C6 51 -0.136721 12.0110 - 52 HC 8 BB6C H13 52 0.117279 1.0080 - 53 HC 8 BB6C H14 53 0.117279 1.0080 - 54 CPos 8 BB6C C5 54 0.143279 12.0110 - 55 HC 8 BB6C H11 55 0.061279 1.0080 - 56 HC 8 BB6C H12 56 0.061279 1.0080 - 57 NTer 8 BB6C N1 57 -0.589721 14.0067 - 58 CPos 9 BB6C C6 58 -0.136771 12.0110 - 59 HC 9 BB6C H13 59 0.117229 1.0080 - 60 HC 9 BB6C H14 60 0.117229 1.0080 - 61 CPos 9 BB6C C5 61 0.143229 12.0110 - 62 HC 9 BB6C H11 62 0.061229 1.0080 - 63 HC 9 BB6C H12 63 0.061229 1.0080 - 64 NTer 9 BB6C N1 64 -0.589771 14.0067 - 65 CPos 10 BB6C C6 65 -0.136861 12.0110 - 66 HC 10 BB6C H13 66 0.117139 1.0080 - 67 HC 10 BB6C H14 67 0.117139 1.0080 - 68 CPos 10 BB6C C5 68 0.143139 12.0110 - 69 HC 10 BB6C H11 69 0.061139 1.0080 - 70 HC 10 BB6C H12 70 0.061139 1.0080 - 71 NTer 10 BB6C N1 71 -0.589861 14.0067 - 72 CPos 11 BB6C C6 72 -0.136811 12.0110 - 73 HC 11 BB6C H13 73 0.117189 1.0080 - 74 HC 11 BB6C H14 74 0.117189 1.0080 - 75 CPos 11 BB6C C5 75 0.143189 12.0110 - 76 HC 11 BB6C H11 76 0.061189 1.0080 - 77 HC 11 BB6C H12 77 0.061189 1.0080 - 78 NTer 11 BB6C N1 78 -0.589811 14.0067 + 30 CPos 5 BB6C C6 30 -0.137266 12.0110 + 31 HC 5 BB6C H13 31 0.116734 1.0080 + 32 HC 5 BB6C H14 32 0.116734 1.0080 + 33 CPos 5 BB6C C5 33 0.142734 12.0110 + 34 HC 5 BB6C H11 34 0.060734 1.0080 + 35 HC 5 BB6C H12 35 0.060734 1.0080 + 36 NTer 5 BB6C N1 36 -0.590266 14.0067 + 37 CPos 6 BB6C C6 37 -0.136736 12.0110 + 38 HC 6 BB6C H13 38 0.117264 1.0080 + 39 HC 6 BB6C H14 39 0.117264 1.0080 + 40 CPos 6 BB6C C5 40 0.143264 12.0110 + 41 HC 6 BB6C H11 41 0.061264 1.0080 + 42 HC 6 BB6C H12 42 0.061264 1.0080 + 43 NTer 6 BB6C N1 43 -0.589736 14.0067 + 44 CPos 7 BB6C C6 44 -0.136786 12.0110 + 45 HC 7 BB6C H13 45 0.117214 1.0080 + 46 HC 7 BB6C H14 46 0.117214 1.0080 + 47 CPos 7 BB6C C5 47 0.143214 12.0110 + 48 HC 7 BB6C H11 48 0.061214 1.0080 + 49 HC 7 BB6C H12 49 0.061214 1.0080 + 50 NTer 7 BB6C N1 50 -0.589786 14.0067 + 51 CPos 8 BB6C C6 51 -0.136861 12.0110 + 52 HC 8 BB6C H13 52 0.117139 1.0080 + 53 HC 8 BB6C H14 53 0.117139 1.0080 + 54 CPos 8 BB6C C5 54 0.143139 12.0110 + 55 HC 8 BB6C H11 55 0.061139 1.0080 + 56 HC 8 BB6C H12 56 0.061139 1.0080 + 57 NTer 8 BB6C N1 57 -0.589861 14.0067 + 58 CPos 9 BB6C C6 58 -0.136736 12.0110 + 59 HC 9 BB6C H13 59 0.117264 1.0080 + 60 HC 9 BB6C H14 60 0.117264 1.0080 + 61 CPos 9 BB6C C5 61 0.143264 12.0110 + 62 HC 9 BB6C H11 62 0.061264 1.0080 + 63 HC 9 BB6C H12 63 0.061264 1.0080 + 64 NTer 9 BB6C N1 64 -0.589736 14.0067 + 65 CPos 10 BB6C C6 65 -0.136786 12.0110 + 66 HC 10 BB6C H13 66 0.117214 1.0080 + 67 HC 10 BB6C H14 67 0.117214 1.0080 + 68 CPos 10 BB6C C5 68 0.143214 12.0110 + 69 HC 10 BB6C H11 69 0.061214 1.0080 + 70 HC 10 BB6C H12 70 0.061214 1.0080 + 71 NTer 10 BB6C N1 71 -0.589786 14.0067 + 72 CPos 11 BB6C C6 72 -0.136861 12.0110 + 73 HC 11 BB6C H13 73 0.117139 1.0080 + 74 HC 11 BB6C H14 74 0.117139 1.0080 + 75 CPos 11 BB6C C5 75 0.143139 12.0110 + 76 HC 11 BB6C H11 76 0.061139 1.0080 + 77 HC 11 BB6C H12 77 0.061139 1.0080 + 78 NTer 11 BB6C N1 78 -0.589861 14.0067 79 CPos 12 BB6C C6 79 -0.136811 12.0110 80 HC 12 BB6C H13 80 0.117189 1.0080 81 HC 12 BB6C H14 81 0.117189 1.0080 @@ -151,660 +151,660 @@ 83 HC 12 BB6C H11 83 0.061189 1.0080 84 HC 12 BB6C H12 84 0.061189 1.0080 85 NTer 12 BB6C N1 85 -0.589811 14.0067 - 86 CPos 13 BB6C C6 86 -0.137442 12.0110 - 87 HC 13 BB6C H13 87 0.116558 1.0080 - 88 HC 13 BB6C H14 88 0.116558 1.0080 - 89 CPos 13 BB6C C5 89 0.142558 12.0110 - 90 HC 13 BB6C H11 90 0.060558 1.0080 - 91 HC 13 BB6C H12 91 0.060558 1.0080 - 92 NTer 13 BB6C N1 92 -0.590442 14.0067 - 93 HS14 14 PHGY H12 93 0.376830 1.0080 - 94 NPri 14 PHGY N2 94 -1.037170 14.0067 - 95 HS14 14 PHGY H11 95 0.376830 1.0080 - 96 CPos 14 PHGY C2 96 0.353830 12.0110 - 97 HC 14 PHGY H3 97 0.024830 1.0080 - 98 HC 14 PHGY H4 98 0.024830 1.0080 - 99 C 14 PHGY C1 99 -0.037170 12.0110 - 100 HC 14 PHGY H1 100 0.064830 1.0080 - 101 HC 14 PHGY H2 101 0.064830 1.0080 - 102 HS14 15 PHGY H12 102 0.377734 1.0080 - 103 NPri 15 PHGY N2 103 -1.036266 14.0067 - 104 HS14 15 PHGY H11 104 0.377734 1.0080 - 105 CPos 15 PHGY C2 105 0.354734 12.0110 - 106 HC 15 PHGY H3 106 0.025734 1.0080 - 107 HC 15 PHGY H4 107 0.025734 1.0080 - 108 C 15 PHGY C1 108 -0.036266 12.0110 - 109 HC 15 PHGY H1 109 0.065734 1.0080 - 110 HC 15 PHGY H2 110 0.065734 1.0080 - 111 HS14 16 PHGY H12 111 0.377699 1.0080 - 112 NPri 16 PHGY N2 112 -1.036301 14.0067 - 113 HS14 16 PHGY H11 113 0.377699 1.0080 - 114 CPos 16 PHGY C2 114 0.354699 12.0110 - 115 HC 16 PHGY H3 115 0.025699 1.0080 - 116 HC 16 PHGY H4 116 0.025699 1.0080 - 117 C 16 PHGY C1 117 -0.036301 12.0110 - 118 HC 16 PHGY H1 118 0.065699 1.0080 - 119 HC 16 PHGY H2 119 0.065699 1.0080 - 120 HS14 17 PHGY H12 120 0.377699 1.0080 - 121 NPri 17 PHGY N2 121 -1.036301 14.0067 - 122 HS14 17 PHGY H11 122 0.377699 1.0080 - 123 CPos 17 PHGY C2 123 0.354699 12.0110 - 124 HC 17 PHGY H3 124 0.025699 1.0080 - 125 HC 17 PHGY H4 125 0.025699 1.0080 - 126 C 17 PHGY C1 126 -0.036301 12.0110 - 127 HC 17 PHGY H1 127 0.065699 1.0080 - 128 HC 17 PHGY H2 128 0.065699 1.0080 - 129 HS14 18 PHGY H12 129 0.377473 1.0080 - 130 NPri 18 PHGY N2 130 -1.036527 14.0067 - 131 HS14 18 PHGY H11 131 0.377473 1.0080 - 132 CPos 18 PHGY C2 132 0.354473 12.0110 - 133 HC 18 PHGY H3 133 0.025473 1.0080 - 134 HC 18 PHGY H4 134 0.025473 1.0080 - 135 C 18 PHGY C1 135 -0.036527 12.0110 - 136 HC 18 PHGY H1 136 0.065473 1.0080 - 137 HC 18 PHGY H2 137 0.065473 1.0080 - 138 HS14 19 PHGY H12 138 0.377437 1.0080 - 139 NPri 19 PHGY N2 139 -1.036563 14.0067 - 140 HS14 19 PHGY H11 140 0.377437 1.0080 - 141 CPos 19 PHGY C2 141 0.354437 12.0110 - 142 HC 19 PHGY H3 142 0.025437 1.0080 - 143 HC 19 PHGY H4 143 0.025437 1.0080 - 144 C 19 PHGY C1 144 -0.036563 12.0110 - 145 HC 19 PHGY H1 145 0.065437 1.0080 - 146 HC 19 PHGY H2 146 0.065437 1.0080 - 147 HS14 20 PHGY H12 147 0.377718 1.0080 - 148 NPri 20 PHGY N2 148 -1.036282 14.0067 - 149 HS14 20 PHGY H11 149 0.377718 1.0080 - 150 CPos 20 PHGY C2 150 0.354718 12.0110 - 151 HC 20 PHGY H3 151 0.025718 1.0080 - 152 HC 20 PHGY H4 152 0.025718 1.0080 - 153 C 20 PHGY C1 153 -0.036282 12.0110 - 154 HC 20 PHGY H1 154 0.065718 1.0080 - 155 HC 20 PHGY H2 155 0.065718 1.0080 - 156 HS14 21 PHGY H12 156 0.377738 1.0080 - 157 NPri 21 PHGY N2 157 -1.036262 14.0067 - 158 HS14 21 PHGY H11 158 0.377738 1.0080 - 159 CPos 21 PHGY C2 159 0.354738 12.0110 - 160 HC 21 PHGY H3 160 0.025738 1.0080 - 161 HC 21 PHGY H4 161 0.025738 1.0080 - 162 C 21 PHGY C1 162 -0.036262 12.0110 - 163 HC 21 PHGY H1 163 0.065738 1.0080 - 164 HC 21 PHGY H2 164 0.065738 1.0080 - 165 HS14 22 PHGY H12 165 0.377702 1.0080 - 166 NPri 22 PHGY N2 166 -1.036298 14.0067 - 167 HS14 22 PHGY H11 167 0.377702 1.0080 - 168 CPos 22 PHGY C2 168 0.354702 12.0110 - 169 HC 22 PHGY H3 169 0.025702 1.0080 - 170 HC 22 PHGY H4 170 0.025702 1.0080 - 171 C 22 PHGY C1 171 -0.036298 12.0110 - 172 HC 22 PHGY H1 172 0.065702 1.0080 - 173 HC 22 PHGY H2 173 0.065702 1.0080 - 174 HS14 23 PHGY H12 174 0.377738 1.0080 - 175 NPri 23 PHGY N2 175 -1.036262 14.0067 - 176 HS14 23 PHGY H11 176 0.377738 1.0080 - 177 CPos 23 PHGY C2 177 0.354738 12.0110 - 178 HC 23 PHGY H3 178 0.025738 1.0080 - 179 HC 23 PHGY H4 179 0.025738 1.0080 - 180 C 23 PHGY C1 180 -0.036262 12.0110 - 181 HC 23 PHGY H1 181 0.065738 1.0080 - 182 HC 23 PHGY H2 182 0.065738 1.0080 - 183 HS14 24 PHGY H12 183 0.377753 1.0080 - 184 NPri 24 PHGY N2 184 -1.036247 14.0067 - 185 HS14 24 PHGY H11 185 0.377753 1.0080 - 186 CPos 24 PHGY C2 186 0.354753 12.0110 - 187 HC 24 PHGY H3 187 0.025753 1.0080 - 188 HC 24 PHGY H4 188 0.025753 1.0080 - 189 C 24 PHGY C1 189 -0.036247 12.0110 - 190 HC 24 PHGY H1 190 0.065753 1.0080 - 191 HC 24 PHGY H2 191 0.065753 1.0080 - 192 HS14 25 PHGY H12 192 0.377718 1.0080 - 193 NPri 25 PHGY N2 193 -1.036282 14.0067 - 194 HS14 25 PHGY H11 194 0.377718 1.0080 - 195 CPos 25 PHGY C2 195 0.354718 12.0110 - 196 HC 25 PHGY H3 196 0.025718 1.0080 - 197 HC 25 PHGY H4 197 0.025718 1.0080 - 198 C 25 PHGY C1 198 -0.036282 12.0110 - 199 HC 25 PHGY H1 199 0.065718 1.0080 - 200 HC 25 PHGY H2 200 0.065718 1.0080 - 201 HS14 26 PHGY H12 201 0.377683 1.0080 - 202 NPri 26 PHGY N2 202 -1.036317 14.0067 - 203 HS14 26 PHGY H11 203 0.377683 1.0080 - 204 CPos 26 PHGY C2 204 0.354683 12.0110 - 205 HC 26 PHGY H3 205 0.025683 1.0080 - 206 HC 26 PHGY H4 206 0.025683 1.0080 - 207 C 26 PHGY C1 207 -0.036317 12.0110 - 208 HC 26 PHGY H1 208 0.065683 1.0080 - 209 HC 26 PHGY H2 209 0.065683 1.0080 - 210 HS14 27 PHGY H12 210 0.377663 1.0080 - 211 NPri 27 PHGY N2 211 -1.036337 14.0067 - 212 HS14 27 PHGY H11 212 0.377663 1.0080 - 213 CPos 27 PHGY C2 213 0.354663 12.0110 - 214 HC 27 PHGY H3 214 0.025663 1.0080 - 215 HC 27 PHGY H4 215 0.025663 1.0080 - 216 C 27 PHGY C1 216 -0.036337 12.0110 - 217 HC 27 PHGY H1 217 0.065663 1.0080 - 218 HC 27 PHGY H2 218 0.065663 1.0080 - 219 HS14 28 PHGY H12 219 0.377683 1.0080 - 220 NPri 28 PHGY N2 220 -1.036317 14.0067 - 221 HS14 28 PHGY H11 221 0.377683 1.0080 - 222 CPos 28 PHGY C2 222 0.354683 12.0110 - 223 HC 28 PHGY H3 223 0.025683 1.0080 - 224 HC 28 PHGY H4 224 0.025683 1.0080 - 225 C 28 PHGY C1 225 -0.036317 12.0110 - 226 HC 28 PHGY H1 226 0.065683 1.0080 - 227 HC 28 PHGY H2 227 0.065683 1.0080 - 228 HS14 29 PHGY H12 228 0.375851 1.0080 - 229 NPri 29 PHGY N2 229 -1.038149 14.0067 - 230 HS14 29 PHGY H11 230 0.375851 1.0080 - 231 CPos 29 PHGY C2 231 0.352851 12.0110 - 232 HC 29 PHGY H3 232 0.023851 1.0080 - 233 HC 29 PHGY H4 233 0.023851 1.0080 - 234 C 29 PHGY C1 234 -0.038149 12.0110 - 235 HC 29 PHGY H1 235 0.063851 1.0080 - 236 HC 29 PHGY H2 236 0.063851 1.0080 + 86 CPos 13 BB6C C6 86 -0.137307 12.0110 + 87 HC 13 BB6C H13 87 0.116693 1.0080 + 88 HC 13 BB6C H14 88 0.116693 1.0080 + 89 CPos 13 BB6C C5 89 0.142693 12.0110 + 90 HC 13 BB6C H11 90 0.060693 1.0080 + 91 HC 13 BB6C H12 91 0.060693 1.0080 + 92 NTer 13 BB6C N1 92 -0.590307 14.0067 + 93 HS14 14 PHGY H12 93 0.376960 1.0080 + 94 NPri 14 PHGY N2 94 -1.037040 14.0067 + 95 HS14 14 PHGY H11 95 0.376960 1.0080 + 96 CPos 14 PHGY C2 96 0.353960 12.0110 + 97 HC 14 PHGY H3 97 0.024960 1.0080 + 98 HC 14 PHGY H4 98 0.024960 1.0080 + 99 C 14 PHGY C1 99 -0.037040 12.0110 + 100 HC 14 PHGY H1 100 0.064960 1.0080 + 101 HC 14 PHGY H2 101 0.064960 1.0080 + 102 HS14 15 PHGY H12 102 0.377742 1.0080 + 103 NPri 15 PHGY N2 103 -1.036258 14.0067 + 104 HS14 15 PHGY H11 104 0.377742 1.0080 + 105 CPos 15 PHGY C2 105 0.354742 12.0110 + 106 HC 15 PHGY H3 106 0.025742 1.0080 + 107 HC 15 PHGY H4 107 0.025742 1.0080 + 108 C 15 PHGY C1 108 -0.036258 12.0110 + 109 HC 15 PHGY H1 109 0.065742 1.0080 + 110 HC 15 PHGY H2 110 0.065742 1.0080 + 111 HS14 16 PHGY H12 111 0.377761 1.0080 + 112 NPri 16 PHGY N2 112 -1.036239 14.0067 + 113 HS14 16 PHGY H11 113 0.377761 1.0080 + 114 CPos 16 PHGY C2 114 0.354761 12.0110 + 115 HC 16 PHGY H3 115 0.025761 1.0080 + 116 HC 16 PHGY H4 116 0.025761 1.0080 + 117 C 16 PHGY C1 117 -0.036239 12.0110 + 118 HC 16 PHGY H1 118 0.065761 1.0080 + 119 HC 16 PHGY H2 119 0.065761 1.0080 + 120 HS14 17 PHGY H12 120 0.377712 1.0080 + 121 NPri 17 PHGY N2 121 -1.036288 14.0067 + 122 HS14 17 PHGY H11 122 0.377712 1.0080 + 123 CPos 17 PHGY C2 123 0.354712 12.0110 + 124 HC 17 PHGY H3 124 0.025712 1.0080 + 125 HC 17 PHGY H4 125 0.025712 1.0080 + 126 C 17 PHGY C1 126 -0.036288 12.0110 + 127 HC 17 PHGY H1 127 0.065712 1.0080 + 128 HC 17 PHGY H2 128 0.065712 1.0080 + 129 HS14 18 PHGY H12 129 0.377663 1.0080 + 130 NPri 18 PHGY N2 130 -1.036337 14.0067 + 131 HS14 18 PHGY H11 131 0.377663 1.0080 + 132 CPos 18 PHGY C2 132 0.354663 12.0110 + 133 HC 18 PHGY H3 133 0.025663 1.0080 + 134 HC 18 PHGY H4 134 0.025663 1.0080 + 135 C 18 PHGY C1 135 -0.036337 12.0110 + 136 HC 18 PHGY H1 136 0.065663 1.0080 + 137 HC 18 PHGY H2 137 0.065663 1.0080 + 138 HS14 19 PHGY H12 138 0.377490 1.0080 + 139 NPri 19 PHGY N2 139 -1.036510 14.0067 + 140 HS14 19 PHGY H11 140 0.377490 1.0080 + 141 CPos 19 PHGY C2 141 0.354490 12.0110 + 142 HC 19 PHGY H3 142 0.025490 1.0080 + 143 HC 19 PHGY H4 143 0.025490 1.0080 + 144 C 19 PHGY C1 144 -0.036510 12.0110 + 145 HC 19 PHGY H1 145 0.065490 1.0080 + 146 HC 19 PHGY H2 146 0.065490 1.0080 + 147 HS14 20 PHGY H12 147 0.377490 1.0080 + 148 NPri 20 PHGY N2 148 -1.036510 14.0067 + 149 HS14 20 PHGY H11 149 0.377490 1.0080 + 150 CPos 20 PHGY C2 150 0.354490 12.0110 + 151 HC 20 PHGY H3 151 0.025490 1.0080 + 152 HC 20 PHGY H4 152 0.025490 1.0080 + 153 C 20 PHGY C1 153 -0.036510 12.0110 + 154 HC 20 PHGY H1 154 0.065490 1.0080 + 155 HC 20 PHGY H2 155 0.065490 1.0080 + 156 HS14 21 PHGY H12 156 0.377693 1.0080 + 157 NPri 21 PHGY N2 157 -1.036307 14.0067 + 158 HS14 21 PHGY H11 158 0.377693 1.0080 + 159 CPos 21 PHGY C2 159 0.354693 12.0110 + 160 HC 21 PHGY H3 160 0.025693 1.0080 + 161 HC 21 PHGY H4 161 0.025693 1.0080 + 162 C 21 PHGY C1 162 -0.036307 12.0110 + 163 HC 21 PHGY H1 163 0.065693 1.0080 + 164 HC 21 PHGY H2 164 0.065693 1.0080 + 165 HS14 22 PHGY H12 165 0.377722 1.0080 + 166 NPri 22 PHGY N2 166 -1.036278 14.0067 + 167 HS14 22 PHGY H11 167 0.377722 1.0080 + 168 CPos 22 PHGY C2 168 0.354722 12.0110 + 169 HC 22 PHGY H3 169 0.025722 1.0080 + 170 HC 22 PHGY H4 170 0.025722 1.0080 + 171 C 22 PHGY C1 171 -0.036278 12.0110 + 172 HC 22 PHGY H1 172 0.065722 1.0080 + 173 HC 22 PHGY H2 173 0.065722 1.0080 + 174 HS14 23 PHGY H12 174 0.377742 1.0080 + 175 NPri 23 PHGY N2 175 -1.036258 14.0067 + 176 HS14 23 PHGY H11 176 0.377742 1.0080 + 177 CPos 23 PHGY C2 177 0.354742 12.0110 + 178 HC 23 PHGY H3 178 0.025742 1.0080 + 179 HC 23 PHGY H4 179 0.025742 1.0080 + 180 C 23 PHGY C1 180 -0.036258 12.0110 + 181 HC 23 PHGY H1 181 0.065742 1.0080 + 182 HC 23 PHGY H2 182 0.065742 1.0080 + 183 HS14 24 PHGY H12 183 0.377732 1.0080 + 184 NPri 24 PHGY N2 184 -1.036268 14.0067 + 185 HS14 24 PHGY H11 185 0.377732 1.0080 + 186 CPos 24 PHGY C2 186 0.354732 12.0110 + 187 HC 24 PHGY H3 187 0.025732 1.0080 + 188 HC 24 PHGY H4 188 0.025732 1.0080 + 189 C 24 PHGY C1 189 -0.036268 12.0110 + 190 HC 24 PHGY H1 190 0.065732 1.0080 + 191 HC 24 PHGY H2 191 0.065732 1.0080 + 192 HS14 25 PHGY H12 192 0.377712 1.0080 + 193 NPri 25 PHGY N2 193 -1.036288 14.0067 + 194 HS14 25 PHGY H11 194 0.377712 1.0080 + 195 CPos 25 PHGY C2 195 0.354712 12.0110 + 196 HC 25 PHGY H3 196 0.025712 1.0080 + 197 HC 25 PHGY H4 197 0.025712 1.0080 + 198 C 25 PHGY C1 198 -0.036288 12.0110 + 199 HC 25 PHGY H1 199 0.065712 1.0080 + 200 HC 25 PHGY H2 200 0.065712 1.0080 + 201 HS14 26 PHGY H12 201 0.377742 1.0080 + 202 NPri 26 PHGY N2 202 -1.036258 14.0067 + 203 HS14 26 PHGY H11 203 0.377742 1.0080 + 204 CPos 26 PHGY C2 204 0.354742 12.0110 + 205 HC 26 PHGY H3 205 0.025742 1.0080 + 206 HC 26 PHGY H4 206 0.025742 1.0080 + 207 C 26 PHGY C1 207 -0.036258 12.0110 + 208 HC 26 PHGY H1 208 0.065742 1.0080 + 209 HC 26 PHGY H2 209 0.065742 1.0080 + 210 HS14 27 PHGY H12 210 0.377732 1.0080 + 211 NPri 27 PHGY N2 211 -1.036268 14.0067 + 212 HS14 27 PHGY H11 212 0.377732 1.0080 + 213 CPos 27 PHGY C2 213 0.354732 12.0110 + 214 HC 27 PHGY H3 214 0.025732 1.0080 + 215 HC 27 PHGY H4 215 0.025732 1.0080 + 216 C 27 PHGY C1 216 -0.036268 12.0110 + 217 HC 27 PHGY H1 217 0.065732 1.0080 + 218 HC 27 PHGY H2 218 0.065732 1.0080 + 219 HS14 28 PHGY H12 219 0.377510 1.0080 + 220 NPri 28 PHGY N2 220 -1.036490 14.0067 + 221 HS14 28 PHGY H11 221 0.377510 1.0080 + 222 CPos 28 PHGY C2 222 0.354510 12.0110 + 223 HC 28 PHGY H3 223 0.025510 1.0080 + 224 HC 28 PHGY H4 224 0.025510 1.0080 + 225 C 28 PHGY C1 225 -0.036490 12.0110 + 226 HC 28 PHGY H1 226 0.065510 1.0080 + 227 HC 28 PHGY H2 227 0.065510 1.0080 + 228 HS14 29 PHGY H12 228 0.375659 1.0080 + 229 NPri 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{"atom_a": 194, "atom_b": 196, "pair_type": 1}, {"atom_a": 199, "atom_b": 204, "pair_type": 1}, {"atom_a": 199, "atom_b": 203, "pair_type": 1}, {"atom_a": 199, "atom_b": 205, "pair_type": 1}, {"atom_a": 200, "atom_b": 207, "pair_type": 1}, {"atom_a": 200, "atom_b": 206, "pair_type": 1}, {"atom_a": 201, "atom_b": 204, "pair_type": 1}, {"atom_a": 201, "atom_b": 205, "pair_type": 1}, {"atom_a": 201, "atom_b": 203, "pair_type": 1}, {"atom_a": 203, "atom_b": 207, "pair_type": 1}, {"atom_a": 203, "atom_b": 206, "pair_type": 1}, {"atom_a": 204, "atom_b": 207, "pair_type": 1}, {"atom_a": 204, "atom_b": 206, "pair_type": 1}, {"atom_a": 209, "atom_b": 213, "pair_type": 1}, {"atom_a": 209, "atom_b": 214, "pair_type": 1}, {"atom_a": 209, "atom_b": 215, "pair_type": 1}, {"atom_a": 210, "atom_b": 216, "pair_type": 1}, {"atom_a": 210, "atom_b": 217, "pair_type": 1}, {"atom_a": 211, "atom_b": 214, "pair_type": 1}, {"atom_a": 211, "atom_b": 213, "pair_type": 1}, {"atom_a": 211, "atom_b": 215, "pair_type": 1}, {"atom_a": 213, "atom_b": 216, "pair_type": 1}, {"atom_a": 213, "atom_b": 217, "pair_type": 1}, {"atom_a": 214, "atom_b": 217, "pair_type": 1}, {"atom_a": 214, "atom_b": 216, "pair_type": 1}, {"atom_a": 219, "atom_b": 225, "pair_type": 1}, {"atom_a": 219, "atom_b": 224, "pair_type": 1}, {"atom_a": 219, "atom_b": 223, "pair_type": 1}, {"atom_a": 220, "atom_b": 227, "pair_type": 1}, {"atom_a": 220, "atom_b": 226, "pair_type": 1}, {"atom_a": 221, "atom_b": 223, "pair_type": 1}, {"atom_a": 221, "atom_b": 224, "pair_type": 1}, {"atom_a": 221, "atom_b": 225, "pair_type": 1}, {"atom_a": 223, "atom_b": 226, "pair_type": 1}, {"atom_a": 223, "atom_b": 227, "pair_type": 1}, {"atom_a": 224, "atom_b": 227, "pair_type": 1}, {"atom_a": 224, "atom_b": 226, "pair_type": 1}, {"atom_a": 229, "atom_b": 234, "pair_type": 1}, {"atom_a": 229, "atom_b": 233, "pair_type": 1}, {"atom_a": 229, "atom_b": 235, "pair_type": 1}, {"atom_a": 230, "atom_b": 236, "pair_type": 1}, {"atom_a": 230, "atom_b": 237, "pair_type": 1}, {"atom_a": 231, "atom_b": 233, "pair_type": 1}, {"atom_a": 231, "atom_b": 234, "pair_type": 1}, {"atom_a": 231, "atom_b": 235, "pair_type": 1}, {"atom_a": 233, "atom_b": 237, "pair_type": 1}, {"atom_a": 233, "atom_b": 236, "pair_type": 1}, {"atom_a": 234, "atom_b": 237, "pair_type": 1}, {"atom_a": 234, "atom_b": 236, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:09 on 2024-12-06 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 6HTJ", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1746623", "; ATB Topology Hash: f4741", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "6HTJ", "nrexcl": 3}}, "junctions": []} \ No newline at end of file +{"topology": {"atoms": [{"atom_id": 1, "atom_type": "CPos", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "C6", "charge_group_num": 16, "partial_charge": 0.021840000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "HC", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "H13", "charge_group_num": 17, "partial_charge": 0.07884, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 3, "atom_type": "HC", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "H14", "charge_group_num": 18, "partial_charge": 0.07884, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 4, "atom_type": "CPos", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "C5", "charge_group_num": 19, "partial_charge": 0.021840000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 5, "atom_type": "HC", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "H11", "charge_group_num": 20, "partial_charge": 0.07884, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 6, "atom_type": "HC", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "H12", "charge_group_num": 21, "partial_charge": 0.07884, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 7, "atom_type": "CPos", "residue_id": 2, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.13802, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 8, "atom_type": "HC", "residue_id": 2, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11598, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 9, "atom_type": "HC", "residue_id": 2, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11598, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 10, "atom_type": "CPos", "residue_id": 2, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14198000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 11, "atom_type": "HC", "residue_id": 2, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.05998, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 12, "atom_type": "HC", "residue_id": 2, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.05998, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 13, "atom_type": "NTer", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "N2", "charge_group_num": 8, "partial_charge": -0.5541600000000001, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 14, "atom_type": "CPos", "residue_id": 3, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.13772, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 15, "atom_type": "HC", "residue_id": 3, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11628000000000001, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 16, "atom_type": "HC", "residue_id": 3, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11628000000000001, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 17, "atom_type": "CPos", "residue_id": 3, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14228000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 18, "atom_type": "HC", "residue_id": 3, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.06028000000000001, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 19, "atom_type": "HC", "residue_id": 3, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.06028000000000001, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 20, "atom_type": "CPos", "residue_id": 4, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.13772, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 21, "atom_type": "HC", "residue_id": 4, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11628, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, 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"atom_b": 213, "pair_type": 1}, {"atom_a": 211, "atom_b": 214, "pair_type": 1}, {"atom_a": 213, "atom_b": 216, "pair_type": 1}, {"atom_a": 213, "atom_b": 217, "pair_type": 1}, {"atom_a": 214, "atom_b": 216, "pair_type": 1}, {"atom_a": 214, "atom_b": 217, "pair_type": 1}, {"atom_a": 219, "atom_b": 225, "pair_type": 1}, {"atom_a": 219, "atom_b": 224, "pair_type": 1}, {"atom_a": 219, "atom_b": 223, "pair_type": 1}, {"atom_a": 220, "atom_b": 226, "pair_type": 1}, {"atom_a": 220, "atom_b": 227, "pair_type": 1}, {"atom_a": 221, "atom_b": 225, "pair_type": 1}, {"atom_a": 221, "atom_b": 224, "pair_type": 1}, {"atom_a": 221, "atom_b": 223, "pair_type": 1}, {"atom_a": 223, "atom_b": 226, "pair_type": 1}, {"atom_a": 223, "atom_b": 227, "pair_type": 1}, {"atom_a": 224, "atom_b": 226, "pair_type": 1}, {"atom_a": 224, "atom_b": 227, "pair_type": 1}, {"atom_a": 229, "atom_b": 234, "pair_type": 1}, {"atom_a": 229, "atom_b": 235, "pair_type": 1}, {"atom_a": 229, "atom_b": 233, "pair_type": 1}, {"atom_a": 230, "atom_b": 236, "pair_type": 1}, {"atom_a": 230, "atom_b": 237, "pair_type": 1}, {"atom_a": 231, "atom_b": 233, "pair_type": 1}, {"atom_a": 231, "atom_b": 234, "pair_type": 1}, {"atom_a": 231, "atom_b": 235, "pair_type": 1}, {"atom_a": 233, "atom_b": 237, "pair_type": 1}, {"atom_a": 233, "atom_b": 236, "pair_type": 1}, {"atom_a": 234, "atom_b": 237, "pair_type": 1}, {"atom_a": 234, "atom_b": 236, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:09 on 2024-12-06 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 6HTJ", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1746623", "; ATB Topology Hash: f4741", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "6HTJ", "nrexcl": 3}}, "junctions": []} \ No newline at end of file diff --git a/data_paper_examples/ethylamine_dendrimer.png b/data_paper_examples/ethylamine_dendrimer.png index 02d31de70e2e7928653d2dec2d506d52faf3046f..400fd91fbb17e2e158bd5bb6fa3ca2b1a820c6a3 100644 GIT binary patch delta 3258 zcmV;r3`O&iu>tWPg`{u$G`M+?SQf}7^R~?c_}d13kU zV;dlqjjoU^am(~ZmzZF@STtEwOq`NomN=MMG}9P^GvKC)8M1JmpBl3Zz|7sSL>HaT z8%!2s;)R*crw_lzf58}=oSsilzWu(Op59%Uxdna|@{xnJ*9afOe7un3M-_jcEuWmc z=JfwX>t9jgKXfr4etyq9fjJ&{ELa7w^59*Ebw2o_@P*)CkM+68twU}h^74@%KwvWh zH7MAC4M7CU5iCaGMrB|Qk0qBM+f6T)5CT!yj;B5jE5M|lM* zDp9!|l}SXaP*siU4piHysYQQn46zhq{iv%)eFGZeXc)$pMl?2I>o#oLjvdWtZovbs 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a/data_paper_examples/pei_linear_polymer.itp +++ b/data_paper_examples/pei_linear_polymer.itp @@ -212,8 +212,8 @@ LHCU 3 [ bonds ] 1 2 2 0.1530 7.1500e+06 2 3 2 0.1470 8.7100e+06 - 3 5 2 0.1470 8.7100e+06 3 4 2 0.1020 1.7782e+07 + 3 5 2 0.1470 8.7100e+06 5 6 2 0.1530 7.1500e+06 6 7 2 0.1470 8.7100e+06 7 9 2 0.1500 8.7100e+06 @@ -223,11 +223,11 @@ LHCU 3 10 11 2 0.1020 1.7782e+07 12 13 2 0.1530 7.1500e+06 13 14 2 0.1470 8.7100e+06 + 14 16 2 0.1500 8.7100e+06 14 15 2 0.1020 1.7782e+07 - 14 16 2 0.1500 7.1500e+06 16 17 2 0.1470 8.7100e+06 - 17 18 2 0.1020 1.7782e+07 17 19 2 0.1470 8.7100e+06 + 17 18 2 0.1020 1.7782e+07 19 20 2 0.1530 7.1500e+06 20 21 2 0.1470 8.7100e+06 21 22 2 0.1020 1.7782e+07 @@ -237,11 +237,11 @@ LHCU 3 24 26 2 0.1470 8.7100e+06 26 27 2 0.1530 7.1500e+06 27 28 2 0.1470 8.7100e+06 - 28 30 2 0.1500 8.7100e+06 28 29 2 0.1020 1.7782e+07 + 28 30 2 0.1500 8.7100e+06 30 31 2 0.1470 8.7100e+06 - 31 33 2 0.1470 8.7100e+06 31 32 2 0.1020 1.7782e+07 + 31 33 2 0.1470 8.7100e+06 33 34 2 0.1530 7.1500e+06 34 35 2 0.1470 8.7100e+06 35 37 2 0.1500 8.7100e+06 @@ -251,11 +251,11 @@ LHCU 3 38 40 2 0.1470 8.7100e+06 40 41 2 0.1530 7.1500e+06 41 42 2 0.1470 8.7100e+06 - 42 44 2 0.1500 8.7100e+06 42 43 2 0.1020 1.7782e+07 + 42 44 2 0.1500 8.7100e+06 44 45 2 0.1470 8.7100e+06 - 45 47 2 0.1470 8.7100e+06 45 46 2 0.1020 1.7782e+07 + 45 47 2 0.1470 8.7100e+06 47 48 2 0.1530 7.1500e+06 48 49 2 0.1470 8.7100e+06 49 51 2 0.1500 8.7100e+06 @@ -265,11 +265,11 @@ LHCU 3 52 54 2 0.1470 8.7100e+06 54 55 2 0.1530 7.1500e+06 55 56 2 0.1470 8.7100e+06 - 56 57 2 0.1020 1.7782e+07 56 58 2 0.1500 8.7100e+06 + 56 57 2 0.1020 1.7782e+07 58 59 2 0.1470 8.7100e+06 - 59 61 2 0.1470 8.7100e+06 59 60 2 0.1020 1.7782e+07 + 59 61 2 0.1470 8.7100e+06 61 62 2 0.1530 7.1500e+06 62 63 2 0.1470 8.7100e+06 63 65 2 0.1500 8.7100e+06 @@ -287,74 +287,74 @@ LHCU 3 75 76 2 0.1530 7.1500e+06 76 77 2 0.1470 8.7100e+06 77 78 2 0.1020 1.7782e+07 - 77 79 2 0.1500 7.1500e+06 + 77 79 2 0.1500 8.7100e+06 79 80 2 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7.1500e+06 139 140 2 0.1470 8.7100e+06 - 140 141 2 0.1020 1.7782e+07 140 142 2 0.1470 8.7100e+06 + 140 141 2 0.1020 1.7782e+07 [ pairs ] - 1 5 1 1 4 1 + 1 5 1 2 6 1 3 7 1 4 6 1 @@ -439,8 +439,8 @@ LHCU 3 [ angles ] 1 2 3 2 111.0000 5.3000e+02 - 2 3 4 2 109.5000 4.2500e+02 2 3 5 2 116.0000 6.2000e+02 + 2 3 4 2 109.5000 4.2500e+02 4 3 5 2 109.5000 4.2500e+02 3 5 6 2 111.0000 5.3000e+02 5 6 7 2 111.0000 5.3000e+02 @@ -448,8 +448,8 @@ LHCU 3 6 7 9 2 116.0000 6.2000e+02 7 9 10 2 111.0000 5.3000e+02 8 7 9 2 109.5000 4.2500e+02 - 9 10 12 2 116.0000 6.2000e+02 9 10 11 2 109.5000 4.2500e+02 + 9 10 12 2 116.0000 6.2000e+02 11 10 12 2 109.5000 4.2500e+02 10 12 13 2 111.0000 5.3000e+02 12 13 14 2 111.0000 5.3000e+02 @@ -457,31 +457,31 @@ LHCU 3 13 14 15 2 109.5000 4.2500e+02 15 14 16 2 109.5000 4.2500e+02 14 16 17 2 111.0000 5.3000e+02 - 16 17 19 2 116.0000 6.2000e+02 16 17 18 2 109.5000 4.2500e+02 - 18 17 19 2 109.5000 4.2500e+02 + 16 17 19 2 116.0000 6.2000e+02 17 19 20 2 111.0000 5.3000e+02 + 18 17 19 2 109.5000 4.2500e+02 19 20 21 2 111.0000 5.3000e+02 - 20 21 23 2 116.0000 6.2000e+02 20 21 22 2 109.5000 4.2500e+02 + 20 21 23 2 116.0000 6.2000e+02 22 21 23 2 109.5000 4.2500e+02 21 23 24 2 111.0000 5.3000e+02 - 23 24 26 2 116.0000 6.2000e+02 23 24 25 2 109.5000 4.2500e+02 + 23 24 26 2 116.0000 6.2000e+02 25 24 26 2 109.5000 4.2500e+02 24 26 27 2 111.0000 5.3000e+02 26 27 28 2 111.0000 5.3000e+02 27 28 30 2 116.0000 6.2000e+02 27 28 29 2 109.5000 4.2500e+02 - 28 30 31 2 111.0000 5.3000e+02 29 28 30 2 109.5000 4.2500e+02 - 30 31 33 2 116.0000 6.2000e+02 + 28 30 31 2 111.0000 5.3000e+02 30 31 32 2 109.5000 4.2500e+02 + 30 31 33 2 116.0000 6.2000e+02 32 31 33 2 109.5000 4.2500e+02 31 33 34 2 111.0000 5.3000e+02 33 34 35 2 111.0000 5.3000e+02 - 34 35 36 2 109.5000 4.2500e+02 34 35 37 2 116.0000 6.2000e+02 + 34 35 36 2 109.5000 4.2500e+02 36 35 37 2 109.5000 4.2500e+02 35 37 38 2 111.0000 5.3000e+02 37 38 39 2 109.5000 4.2500e+02 @@ -493,15 +493,15 @@ LHCU 3 41 42 43 2 109.5000 4.2500e+02 43 42 44 2 109.5000 4.2500e+02 42 44 45 2 111.0000 5.3000e+02 - 44 45 46 2 109.5000 4.2500e+02 44 45 47 2 116.0000 6.2000e+02 - 45 47 48 2 111.0000 5.3000e+02 + 44 45 46 2 109.5000 4.2500e+02 46 45 47 2 109.5000 4.2500e+02 + 45 47 48 2 111.0000 5.3000e+02 47 48 49 2 111.0000 5.3000e+02 - 48 49 50 2 109.5000 4.2500e+02 48 49 51 2 116.0000 6.2000e+02 - 50 49 51 2 109.5000 4.2500e+02 + 48 49 50 2 109.5000 4.2500e+02 49 51 52 2 111.0000 5.3000e+02 + 50 49 51 2 109.5000 4.2500e+02 51 52 53 2 109.5000 4.2500e+02 51 52 54 2 116.0000 6.2000e+02 53 52 54 2 109.5000 4.2500e+02 @@ -509,19 +509,19 @@ LHCU 3 54 55 56 2 111.0000 5.3000e+02 55 56 57 2 109.5000 4.2500e+02 55 56 58 2 116.0000 6.2000e+02 - 57 56 58 2 109.5000 4.2500e+02 56 58 59 2 111.0000 5.3000e+02 + 57 56 58 2 109.5000 4.2500e+02 58 59 61 2 116.0000 6.2000e+02 58 59 60 2 109.5000 4.2500e+02 - 59 61 62 2 111.0000 5.3000e+02 60 59 61 2 109.5000 4.2500e+02 + 59 61 62 2 111.0000 5.3000e+02 61 62 63 2 111.0000 5.3000e+02 - 62 63 64 2 109.5000 4.2500e+02 62 63 65 2 116.0000 6.2000e+02 + 62 63 64 2 109.5000 4.2500e+02 64 63 65 2 109.5000 4.2500e+02 63 65 66 2 111.0000 5.3000e+02 - 65 66 68 2 116.0000 6.2000e+02 65 66 67 2 109.5000 4.2500e+02 + 65 66 68 2 116.0000 6.2000e+02 67 66 68 2 109.5000 4.2500e+02 66 68 69 2 111.0000 5.3000e+02 68 69 70 2 111.0000 5.3000e+02 @@ -543,28 +543,28 @@ LHCU 3 81 80 82 2 109.5000 4.2500e+02 80 82 83 2 111.0000 5.3000e+02 82 83 84 2 111.0000 5.3000e+02 - 83 84 86 2 116.0000 6.2000e+02 83 84 85 2 109.5000 4.2500e+02 - 84 86 87 2 111.0000 5.3000e+02 + 83 84 86 2 116.0000 6.2000e+02 85 84 86 2 109.5000 4.2500e+02 - 86 87 89 2 116.0000 6.2000e+02 + 84 86 87 2 111.0000 5.3000e+02 86 87 88 2 109.5000 4.2500e+02 + 86 87 89 2 116.0000 6.2000e+02 88 87 89 2 109.5000 4.2500e+02 87 89 90 2 111.0000 5.3000e+02 89 90 91 2 111.0000 5.3000e+02 90 91 92 2 109.5000 4.2500e+02 90 91 93 2 116.0000 6.2000e+02 - 91 93 94 2 111.0000 5.3000e+02 92 91 93 2 109.5000 4.2500e+02 - 93 94 95 2 109.5000 4.2500e+02 + 91 93 94 2 111.0000 5.3000e+02 93 94 96 2 116.0000 6.2000e+02 - 94 96 97 2 111.0000 5.3000e+02 + 93 94 95 2 109.5000 4.2500e+02 95 94 96 2 109.5000 4.2500e+02 + 94 96 97 2 111.0000 5.3000e+02 96 97 98 2 111.0000 5.3000e+02 97 98 99 2 109.5000 4.2500e+02 97 98 100 2 116.0000 6.2000e+02 - 98 100 101 2 111.0000 5.3000e+02 99 98 100 2 109.5000 4.2500e+02 + 98 100 101 2 111.0000 5.3000e+02 100 101 102 2 109.5000 4.2500e+02 100 101 103 2 116.0000 6.2000e+02 102 101 103 2 109.5000 4.2500e+02 @@ -574,13 +574,13 @@ LHCU 3 104 105 107 2 116.0000 6.2000e+02 106 105 107 2 109.5000 4.2500e+02 105 107 108 2 111.0000 5.3000e+02 - 107 108 109 2 109.5000 4.2500e+02 107 108 110 2 116.0000 6.2000e+02 + 107 108 109 2 109.5000 4.2500e+02 109 108 110 2 109.5000 4.2500e+02 108 110 111 2 111.0000 5.3000e+02 110 111 112 2 111.0000 5.3000e+02 - 111 112 114 2 116.0000 6.2000e+02 111 112 113 2 109.5000 4.2500e+02 + 111 112 114 2 116.0000 6.2000e+02 113 112 114 2 109.5000 4.2500e+02 112 114 115 2 111.0000 5.3000e+02 114 115 116 2 109.5000 4.2500e+02 @@ -592,13 +592,13 @@ LHCU 3 118 119 121 2 116.0000 6.2000e+02 120 119 121 2 109.5000 4.2500e+02 119 121 122 2 111.0000 5.3000e+02 - 121 122 124 2 116.0000 6.2000e+02 121 122 123 2 109.5000 4.2500e+02 - 122 124 125 2 111.0000 5.3000e+02 + 121 122 124 2 116.0000 6.2000e+02 123 122 124 2 109.5000 4.2500e+02 + 122 124 125 2 111.0000 5.3000e+02 124 125 126 2 111.0000 5.3000e+02 - 125 126 127 2 109.5000 4.2500e+02 125 126 128 2 116.0000 6.2000e+02 + 125 126 127 2 109.5000 4.2500e+02 126 128 129 2 111.0000 5.3000e+02 127 126 128 2 109.5000 4.2500e+02 128 129 131 2 116.0000 6.2000e+02 @@ -610,8 +610,8 @@ LHCU 3 132 133 134 2 109.5000 4.2500e+02 133 135 136 2 111.0000 5.3000e+02 134 133 135 2 109.5000 4.2500e+02 - 135 136 138 2 116.0000 6.2000e+02 135 136 137 2 109.5000 4.2500e+02 + 135 136 138 2 116.0000 6.2000e+02 137 136 138 2 109.5000 4.2500e+02 136 138 139 2 111.0000 5.3000e+02 138 139 140 2 111.0000 5.3000e+02 diff --git a/data_paper_examples/pei_linear_polymer.json b/data_paper_examples/pei_linear_polymer.json index 91b6390..b62e06c 100644 --- a/data_paper_examples/pei_linear_polymer.json +++ b/data_paper_examples/pei_linear_polymer.json @@ -1 +1 @@ -{"topology": {"atoms": [{"atom_id": 1, "atom_type": "CH3", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C62", "charge_group_num": 1, "partial_charge": 0.013437500000000005, "mass": 15.035, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C51", "charge_group_num": 2, "partial_charge": 0.2134375, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 3, "atom_type": "NOpt", "residue_id": 1, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6855625, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 4, "atom_type": "HS14", "residue_id": 1, "residue_name": "LHCU", 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41, "pair_type": 1}, {"atom_a": 40, "atom_b": 42, "pair_type": 1}, {"atom_a": 44, "atom_b": 48, "pair_type": 1}, {"atom_a": 45, "atom_b": 50, "pair_type": 1}, {"atom_a": 46, "atom_b": 48, "pair_type": 1}, {"atom_a": 47, "atom_b": 49, "pair_type": 1}, {"atom_a": 51, "atom_b": 55, "pair_type": 1}, {"atom_a": 52, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 55, "pair_type": 1}, {"atom_a": 54, "atom_b": 56, "pair_type": 1}, {"atom_a": 58, "atom_b": 62, "pair_type": 1}, {"atom_a": 59, "atom_b": 64, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 61, "atom_b": 63, "pair_type": 1}, {"atom_a": 65, "atom_b": 69, "pair_type": 1}, {"atom_a": 66, "atom_b": 71, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 68, "atom_b": 70, "pair_type": 1}, {"atom_a": 72, "atom_b": 76, "pair_type": 1}, {"atom_a": 73, "atom_b": 78, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 75, "atom_b": 77, "pair_type": 1}, {"atom_a": 79, "atom_b": 83, "pair_type": 1}, {"atom_a": 80, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 82, "atom_b": 84, "pair_type": 1}, {"atom_a": 86, "atom_b": 90, "pair_type": 1}, {"atom_a": 87, "atom_b": 92, "pair_type": 1}, {"atom_a": 88, "atom_b": 90, "pair_type": 1}, {"atom_a": 89, "atom_b": 91, "pair_type": 1}, {"atom_a": 93, "atom_b": 97, "pair_type": 1}, {"atom_a": 94, "atom_b": 99, "pair_type": 1}, {"atom_a": 95, "atom_b": 97, "pair_type": 1}, {"atom_a": 96, "atom_b": 98, "pair_type": 1}, {"atom_a": 100, "atom_b": 104, "pair_type": 1}, {"atom_a": 101, "atom_b": 106, "pair_type": 1}, {"atom_a": 102, "atom_b": 104, "pair_type": 1}, {"atom_a": 103, "atom_b": 105, "pair_type": 1}, {"atom_a": 107, "atom_b": 111, "pair_type": 1}, {"atom_a": 108, "atom_b": 113, "pair_type": 1}, {"atom_a": 109, "atom_b": 111, "pair_type": 1}, {"atom_a": 110, "atom_b": 112, "pair_type": 1}, {"atom_a": 114, "atom_b": 118, "pair_type": 1}, {"atom_a": 115, "atom_b": 120, "pair_type": 1}, {"atom_a": 116, "atom_b": 118, "pair_type": 1}, {"atom_a": 117, "atom_b": 119, "pair_type": 1}, {"atom_a": 121, "atom_b": 125, "pair_type": 1}, {"atom_a": 122, "atom_b": 127, "pair_type": 1}, {"atom_a": 123, "atom_b": 125, "pair_type": 1}, {"atom_a": 124, "atom_b": 126, "pair_type": 1}, {"atom_a": 128, "atom_b": 132, "pair_type": 1}, {"atom_a": 129, "atom_b": 133, "pair_type": 1}, {"atom_a": 130, "atom_b": 132, "pair_type": 1}, {"atom_a": 131, "atom_b": 134, "pair_type": 1}, {"atom_a": 137, "atom_b": 141, "pair_type": 1}, {"atom_a": 138, "atom_b": 142, "pair_type": 1}, {"atom_a": 139, "atom_b": 141, "pair_type": 1}, {"atom_a": 140, "atom_b": 144, "pair_type": 1}, {"atom_a": 140, "atom_b": 143, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:05 on 2024-12-13 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : LHCU", "; Output : UNITED ATOM topology", ";\tUse in conjunction with the corresponding united atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1707355", "; ATB Topology Hash: f968d", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "LHCU", "nrexcl": 3}}, "junctions": [{"name": "to", "monomer_atom": "C51", "residue_atom": "C62"}, {"name": "from", "monomer_atom": "N7", "residue_atom": "C6"}]} \ No newline at end of file +{"topology": {"atoms": [{"atom_id": 1, "atom_type": "CH3", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C62", "charge_group_num": 1, "partial_charge": 0.013437500000000005, "mass": 15.035, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C51", "charge_group_num": 2, "partial_charge": 0.2134375, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 3, "atom_type": "NOpt", "residue_id": 1, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6855625, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 4, "atom_type": "HS14", "residue_id": 1, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.30443749999999997, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 5, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.2104375, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 6, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.2254375, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 7, "atom_type": "HS14", "residue_id": 1, "residue_name": "LHCU", "atom_name": "H21", "charge_group_num": 8, "partial_charge": 0.3184375, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 8, "atom_type": "NOpt", "residue_id": 1, "residue_name": "LHCU", "atom_name": "N7", "charge_group_num": 7, "partial_charge": -0.6985625, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 9, "atom_type": "CH2", "residue_id": 2, "residue_name": "LHCU", "atom_name": "C51", "charge_group_num": 2, "partial_charge": 0.22753333333333334, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 10, "atom_type": "NOpt", "residue_id": 2, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6714666666666667, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 11, "atom_type": "HS14", "residue_id": 2, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.31853333333333333, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 12, "atom_type": "CH2", "residue_id": 2, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.22453333333333333, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 13, "atom_type": "CH2", "residue_id": 2, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.23953333333333335, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 14, "atom_type": "HS14", "residue_id": 2, "residue_name": "LHCU", "atom_name": "H21", "charge_group_num": 8, "partial_charge": 0.33253333333333335, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 15, "atom_type": "NOpt", "residue_id": 2, "residue_name": "LHCU", "atom_name": "N7", "charge_group_num": 7, "partial_charge": -0.6844666666666667, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 16, "atom_type": "CH2", "residue_id": 3, "residue_name": "LHCU", "atom_name": "C51", "charge_group_num": 2, "partial_charge": 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80, "atom_b": 82, "atom_c": 83, "atom_d": 85, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 82, "atom_b": 83, "atom_c": 85, "atom_d": 86, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 85, "atom_b": 86, "atom_c": 87, "atom_d": 89, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 86, "atom_b": 87, "atom_c": 89, "atom_d": 90, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 87, "atom_b": 89, "atom_c": 90, "atom_d": 92, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 89, "atom_b": 90, "atom_c": 92, "atom_d": 93, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 92, "atom_b": 93, "atom_c": 94, "atom_d": 96, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 93, "atom_b": 94, "atom_c": 96, "atom_d": 97, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 94, "atom_b": 96, "atom_c": 97, "atom_d": 99, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 96, "atom_b": 97, "atom_c": 99, "atom_d": 100, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 99, "atom_b": 100, "atom_c": 101, "atom_d": 103, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 100, "atom_b": 101, "atom_c": 103, "atom_d": 104, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 101, "atom_b": 103, "atom_c": 104, "atom_d": 106, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 103, "atom_b": 104, "atom_c": 106, "atom_d": 107, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 106, "atom_b": 107, "atom_c": 108, "atom_d": 110, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 107, "atom_b": 108, "atom_c": 110, "atom_d": 111, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 108, "atom_b": 110, "atom_c": 111, "atom_d": 113, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 110, "atom_b": 111, "atom_c": 113, "atom_d": 114, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 113, "atom_b": 114, "atom_c": 115, "atom_d": 117, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 114, "atom_b": 115, "atom_c": 117, "atom_d": 118, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 115, "atom_b": 117, "atom_c": 118, "atom_d": 120, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 117, "atom_b": 118, "atom_c": 120, "atom_d": 121, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 120, "atom_b": 121, "atom_c": 122, "atom_d": 124, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 121, "atom_b": 122, "atom_c": 124, "atom_d": 125, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 122, "atom_b": 124, "atom_c": 125, "atom_d": 127, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 124, "atom_b": 125, "atom_c": 127, "atom_d": 128, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 127, "atom_b": 128, "atom_c": 129, "atom_d": 131, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 128, "atom_b": 129, "atom_c": 131, "atom_d": 132, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 129, "atom_b": 131, "atom_c": 132, "atom_d": 133, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 131, "atom_b": 132, "atom_c": 133, "atom_d": 137, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 133, "atom_b": 137, "atom_c": 138, "atom_d": 140, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 137, "atom_b": 138, "atom_c": 140, "atom_d": 141, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 138, "atom_b": 140, "atom_c": 141, "atom_d": 142, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 140, "atom_b": 141, "atom_c": 142, "atom_d": 144, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}], "pairs": [{"atom_a": 1, "atom_b": 4, "pair_type": 1}, {"atom_a": 1, "atom_b": 5, "pair_type": 1}, {"atom_a": 2, "atom_b": 6, "pair_type": 1}, {"atom_a": 3, "atom_b": 8, "pair_type": 1}, {"atom_a": 4, "atom_b": 6, "pair_type": 1}, {"atom_a": 5, "atom_b": 7, "pair_type": 1}, {"atom_a": 9, "atom_b": 13, "pair_type": 1}, {"atom_a": 10, "atom_b": 15, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 12, "atom_b": 14, "pair_type": 1}, {"atom_a": 16, "atom_b": 20, "pair_type": 1}, {"atom_a": 17, "atom_b": 22, "pair_type": 1}, {"atom_a": 18, "atom_b": 20, "pair_type": 1}, {"atom_a": 19, "atom_b": 21, "pair_type": 1}, {"atom_a": 23, "atom_b": 27, "pair_type": 1}, {"atom_a": 24, "atom_b": 29, "pair_type": 1}, {"atom_a": 25, "atom_b": 27, "pair_type": 1}, {"atom_a": 26, "atom_b": 28, "pair_type": 1}, {"atom_a": 30, "atom_b": 34, "pair_type": 1}, {"atom_a": 31, "atom_b": 36, "pair_type": 1}, {"atom_a": 32, "atom_b": 34, "pair_type": 1}, {"atom_a": 33, "atom_b": 35, "pair_type": 1}, {"atom_a": 37, "atom_b": 41, "pair_type": 1}, {"atom_a": 38, "atom_b": 43, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 40, "atom_b": 42, "pair_type": 1}, {"atom_a": 44, "atom_b": 48, "pair_type": 1}, {"atom_a": 45, "atom_b": 50, "pair_type": 1}, {"atom_a": 46, "atom_b": 48, "pair_type": 1}, {"atom_a": 47, "atom_b": 49, "pair_type": 1}, {"atom_a": 51, "atom_b": 55, "pair_type": 1}, {"atom_a": 52, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 55, "pair_type": 1}, {"atom_a": 54, "atom_b": 56, "pair_type": 1}, {"atom_a": 58, "atom_b": 62, "pair_type": 1}, {"atom_a": 59, "atom_b": 64, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 61, "atom_b": 63, "pair_type": 1}, {"atom_a": 65, "atom_b": 69, "pair_type": 1}, {"atom_a": 66, "atom_b": 71, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 68, "atom_b": 70, "pair_type": 1}, {"atom_a": 72, "atom_b": 76, "pair_type": 1}, {"atom_a": 73, "atom_b": 78, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 75, "atom_b": 77, "pair_type": 1}, {"atom_a": 79, "atom_b": 83, "pair_type": 1}, {"atom_a": 80, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 82, "atom_b": 84, "pair_type": 1}, {"atom_a": 86, "atom_b": 90, "pair_type": 1}, {"atom_a": 87, "atom_b": 92, "pair_type": 1}, {"atom_a": 88, "atom_b": 90, "pair_type": 1}, {"atom_a": 89, "atom_b": 91, "pair_type": 1}, {"atom_a": 93, "atom_b": 97, "pair_type": 1}, {"atom_a": 94, "atom_b": 99, "pair_type": 1}, {"atom_a": 95, "atom_b": 97, "pair_type": 1}, {"atom_a": 96, "atom_b": 98, "pair_type": 1}, {"atom_a": 100, "atom_b": 104, "pair_type": 1}, {"atom_a": 101, "atom_b": 106, "pair_type": 1}, {"atom_a": 102, "atom_b": 104, "pair_type": 1}, {"atom_a": 103, "atom_b": 105, "pair_type": 1}, {"atom_a": 107, "atom_b": 111, "pair_type": 1}, {"atom_a": 108, "atom_b": 113, "pair_type": 1}, {"atom_a": 109, "atom_b": 111, "pair_type": 1}, {"atom_a": 110, "atom_b": 112, "pair_type": 1}, {"atom_a": 114, "atom_b": 118, "pair_type": 1}, {"atom_a": 115, "atom_b": 120, "pair_type": 1}, {"atom_a": 116, "atom_b": 118, "pair_type": 1}, {"atom_a": 117, "atom_b": 119, "pair_type": 1}, {"atom_a": 121, "atom_b": 125, "pair_type": 1}, {"atom_a": 122, "atom_b": 127, "pair_type": 1}, {"atom_a": 123, "atom_b": 125, "pair_type": 1}, {"atom_a": 124, "atom_b": 126, "pair_type": 1}, {"atom_a": 128, "atom_b": 132, "pair_type": 1}, {"atom_a": 129, "atom_b": 133, "pair_type": 1}, {"atom_a": 130, "atom_b": 132, "pair_type": 1}, {"atom_a": 131, "atom_b": 134, "pair_type": 1}, {"atom_a": 137, "atom_b": 141, "pair_type": 1}, {"atom_a": 138, "atom_b": 142, "pair_type": 1}, {"atom_a": 139, "atom_b": 141, "pair_type": 1}, {"atom_a": 140, "atom_b": 144, "pair_type": 1}, {"atom_a": 140, "atom_b": 143, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:05 on 2024-12-13 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : LHCU", "; Output : UNITED ATOM topology", ";\tUse in conjunction with the corresponding united atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1707355", "; ATB Topology Hash: f968d", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "LHCU", "nrexcl": 3}}, "junctions": [{"name": "to", "monomer_atom": "C51", "residue_atom": "C62"}, {"name": "from", "monomer_atom": "N7", "residue_atom": "C6"}]} \ No newline at end of file diff --git a/data_paper_examples/polyester.itp b/data_paper_examples/polyester.itp index 3f2bdcb..288c74d 100644 --- a/data_paper_examples/polyester.itp +++ b/data_paper_examples/polyester.itp @@ -190,94 +190,94 @@ E6SD 3 [ bonds ] 1 2 2 0.0972 1.9581e+07 2 3 2 0.1430 8.1800e+06 - 3 6 2 0.1520 5.4300e+06 3 4 2 0.1090 1.2300e+07 + 3 6 2 0.1520 5.4300e+06 3 5 2 0.1090 1.2300e+07 6 9 2 0.1430 8.1800e+06 - 6 8 2 0.1090 1.2300e+07 6 7 2 0.1090 1.2300e+07 + 6 8 2 0.1090 1.2300e+07 9 10 2 0.1161 1.9581e+07 10 11 2 0.1220 2.2843e+07 10 12 2 0.1500 8.3700e+06 - 12 20 2 0.1400 8.5400e+06 12 13 2 0.1400 8.5400e+06 - 13 14 2 0.1090 1.2300e+07 + 12 20 2 0.1400 8.5400e+06 13 15 2 0.1390 8.6600e+06 - 15 16 2 0.1090 1.2300e+07 + 13 14 2 0.1090 1.2300e+07 15 17 2 0.1400 8.5400e+06 - 17 22 2 0.1500 8.3700e+06 + 15 16 2 0.1090 1.2300e+07 17 18 2 0.1400 8.5400e+06 - 18 19 2 0.1090 1.2300e+07 + 17 22 2 0.1500 8.3700e+06 18 20 2 0.1390 8.6600e+06 + 18 19 2 0.1090 1.2300e+07 20 21 2 0.1090 1.2300e+07 22 23 2 0.1220 2.2843e+07 - 22 24 2 0.1161 1.9581e+07 + 22 24 2 0.1161 1.0300e+07 24 25 2 0.1430 8.1800e+06 - 25 27 2 0.1090 1.2300e+07 25 28 2 0.1520 5.4300e+06 + 25 27 2 0.1090 1.2300e+07 25 26 2 0.1090 1.2300e+07 28 30 2 0.1090 1.2300e+07 - 28 29 2 0.1090 1.2300e+07 28 31 2 0.1430 8.1800e+06 - 31 32 2 0.1161 1.0300e+07 + 28 29 2 0.1090 1.2300e+07 + 31 32 2 0.1161 1.9581e+07 32 34 2 0.1500 8.3700e+06 32 33 2 0.1220 2.2843e+07 - 34 35 2 0.1400 8.5400e+06 34 42 2 0.1400 8.5400e+06 - 35 36 2 0.1090 1.2300e+07 + 34 35 2 0.1400 8.5400e+06 35 37 2 0.1390 8.6600e+06 + 35 36 2 0.1090 1.2300e+07 37 39 2 0.1400 8.5400e+06 37 38 2 0.1090 1.2300e+07 - 39 44 2 0.1500 8.3700e+06 39 40 2 0.1400 8.5400e+06 + 39 44 2 0.1500 8.3700e+06 40 41 2 0.1090 1.2300e+07 40 42 2 0.1390 8.6600e+06 42 43 2 0.1090 1.2300e+07 - 44 46 2 0.1161 1.0300e+07 44 45 2 0.1220 2.2843e+07 + 44 46 2 0.1161 1.0300e+07 46 47 2 0.1430 8.1800e+06 - 47 48 2 0.1090 1.2300e+07 - 47 49 2 0.1090 1.2300e+07 47 50 2 0.1520 5.4300e+06 - 50 51 2 0.1090 1.2300e+07 + 47 49 2 0.1090 1.2300e+07 + 47 48 2 0.1090 1.2300e+07 50 53 2 0.1430 8.1800e+06 50 52 2 0.1090 1.2300e+07 - 53 54 2 0.1161 1.0300e+07 + 50 51 2 0.1090 1.2300e+07 + 53 54 2 0.1161 1.9581e+07 54 55 2 0.1220 2.2843e+07 54 56 2 0.1500 8.3700e+06 56 57 2 0.1400 8.5400e+06 56 64 2 0.1400 8.5400e+06 - 57 59 2 0.1390 8.6600e+06 57 58 2 0.1090 1.2300e+07 - 59 61 2 0.1400 8.5400e+06 + 57 59 2 0.1390 8.6600e+06 59 60 2 0.1090 1.2300e+07 + 59 61 2 0.1400 8.5400e+06 61 66 2 0.1500 8.3700e+06 61 62 2 0.1400 8.5400e+06 - 62 63 2 0.1090 1.2300e+07 62 64 2 0.1390 8.6600e+06 + 62 63 2 0.1090 1.2300e+07 64 65 2 0.1090 1.2300e+07 66 67 2 0.1220 2.2843e+07 - 66 68 2 0.1161 1.9581e+07 + 66 68 2 0.1161 1.0300e+07 68 69 2 0.1430 8.1800e+06 69 70 2 0.1090 1.2300e+07 69 71 2 0.1090 1.2300e+07 69 72 2 0.1520 5.4300e+06 - 72 73 2 0.1090 1.2300e+07 72 75 2 0.1430 8.1800e+06 72 74 2 0.1090 1.2300e+07 - 75 76 2 0.1161 1.0300e+07 - 76 77 2 0.1220 2.2843e+07 + 72 73 2 0.1090 1.2300e+07 + 75 76 2 0.1161 1.9581e+07 76 78 2 0.1500 8.3700e+06 - 78 86 2 0.1400 8.5400e+06 + 76 77 2 0.1220 2.2843e+07 78 79 2 0.1400 8.5400e+06 - 79 80 2 0.1090 1.2300e+07 + 78 86 2 0.1400 8.5400e+06 79 81 2 0.1390 8.6600e+06 + 79 80 2 0.1090 1.2300e+07 81 82 2 0.1090 1.2300e+07 81 83 2 0.1400 8.5400e+06 - 83 88 2 0.1500 8.3700e+06 83 84 2 0.1400 8.5400e+06 - 84 86 2 0.1390 8.6600e+06 + 83 88 2 0.1500 8.3700e+06 84 85 2 0.1090 1.2300e+07 + 84 86 2 0.1390 8.6600e+06 86 87 2 0.1090 1.2300e+07 88 90 2 0.1161 1.0300e+07 88 89 2 0.1220 2.2843e+07 @@ -288,11 +288,11 @@ E6SD 3 94 95 2 0.1090 1.2300e+07 94 96 2 0.1090 1.2300e+07 94 97 2 0.1430 8.1800e+06 - 97 98 2 0.1161 1.0300e+07 + 97 98 2 0.1161 1.9581e+07 98 100 2 0.1500 8.3700e+06 98 99 2 0.1220 2.2843e+07 - 100 108 2 0.1400 8.5400e+06 100 101 2 0.1400 8.5400e+06 + 100 108 2 0.1400 8.5400e+06 101 102 2 0.1090 1.2300e+07 101 103 2 0.1390 8.6600e+06 103 105 2 0.1400 8.5400e+06 @@ -302,74 +302,74 @@ E6SD 3 106 107 2 0.1090 1.2300e+07 106 108 2 0.1390 8.6600e+06 108 109 2 0.1090 1.2300e+07 - 110 112 2 0.1161 1.9581e+07 + 110 112 2 0.1161 1.0300e+07 110 111 2 0.1220 2.2843e+07 112 113 2 0.1430 8.1800e+06 113 116 2 0.1520 5.4300e+06 113 114 2 0.1090 1.2300e+07 113 115 2 0.1090 1.2300e+07 + 116 118 2 0.1090 1.2300e+07 116 119 2 0.1430 8.1800e+06 116 117 2 0.1090 1.2300e+07 - 116 118 2 0.1090 1.2300e+07 119 120 2 0.0972 1.9581e+07 [ pairs ] 1 5 1 - 1 4 1 1 6 1 + 1 4 1 + 2 8 1 2 7 1 2 9 1 - 2 8 1 4 9 1 4 7 1 4 8 1 - 5 9 1 5 7 1 + 5 9 1 5 8 1 - 10 15 1 - 10 18 1 10 21 1 + 10 15 1 10 14 1 + 10 18 1 11 13 1 11 20 1 - 12 16 1 12 19 1 + 12 16 1 13 22 1 13 21 1 - 14 17 1 - 14 16 1 14 20 1 + 14 16 1 + 14 17 1 15 23 1 15 19 1 - 16 22 1 16 18 1 + 16 22 1 17 21 1 18 23 1 19 22 1 19 21 1 20 22 1 - 24 30 1 24 31 1 + 24 30 1 24 29 1 - 26 30 1 26 29 1 26 31 1 - 27 30 1 - 27 29 1 + 26 30 1 27 31 1 + 27 29 1 + 27 30 1 + 32 43 1 32 40 1 32 36 1 - 32 43 1 32 37 1 33 35 1 33 42 1 - 34 41 1 34 38 1 - 35 44 1 + 34 41 1 35 43 1 - 36 39 1 - 36 38 1 + 35 44 1 36 42 1 + 36 38 1 + 36 39 1 37 45 1 37 41 1 38 44 1 @@ -383,45 +383,45 @@ E6SD 3 46 51 1 46 53 1 48 52 1 - 48 51 1 48 53 1 - 49 53 1 + 48 51 1 49 52 1 + 49 53 1 49 51 1 - 54 59 1 54 62 1 54 58 1 54 65 1 - 55 64 1 + 54 59 1 55 57 1 + 55 64 1 56 60 1 56 63 1 - 57 65 1 57 66 1 + 57 65 1 58 64 1 - 58 60 1 58 61 1 + 58 60 1 59 63 1 59 67 1 60 66 1 60 62 1 61 65 1 62 67 1 - 63 66 1 63 65 1 + 63 66 1 64 66 1 68 74 1 68 73 1 68 75 1 70 75 1 - 70 73 1 70 74 1 - 71 74 1 + 70 73 1 71 75 1 71 73 1 - 76 81 1 - 76 87 1 + 71 74 1 76 80 1 + 76 87 1 + 76 81 1 76 84 1 77 79 1 77 86 1 @@ -429,224 +429,224 @@ E6SD 3 78 85 1 79 87 1 79 88 1 - 80 86 1 80 83 1 + 80 86 1 80 82 1 81 85 1 81 89 1 - 82 88 1 82 84 1 + 82 88 1 83 87 1 84 89 1 - 85 87 1 85 88 1 + 85 87 1 86 88 1 - 90 95 1 90 97 1 90 96 1 - 92 97 1 - 92 95 1 + 90 95 1 92 96 1 + 92 95 1 + 92 97 1 93 96 1 93 95 1 93 97 1 - 98 109 1 98 106 1 - 98 102 1 98 103 1 + 98 102 1 + 98 109 1 99 108 1 99 101 1 100 104 1 100 107 1 - 101 110 1 101 109 1 + 101 110 1 + 102 104 1 102 108 1 102 105 1 - 102 104 1 - 103 111 1 103 107 1 - 104 110 1 + 103 111 1 104 106 1 + 104 110 1 105 109 1 106 111 1 - 107 110 1 107 109 1 + 107 110 1 108 110 1 + 112 119 1 112 117 1 112 118 1 - 112 119 1 113 120 1 114 119 1 114 118 1 114 117 1 115 119 1 - 115 117 1 115 118 1 + 115 117 1 117 120 1 118 120 1 [ angles ] 1 2 3 2 109.5000 4.5000e+02 - 2 3 4 2 107.5700 4.8400e+02 - 2 3 6 2 109.5000 5.2000e+02 2 3 5 2 107.5700 4.8400e+02 - 5 3 6 2 109.6000 4.5000e+02 + 2 3 6 2 109.5000 5.2000e+02 + 2 3 4 2 107.5700 4.8400e+02 4 3 6 2 109.6000 4.5000e+02 + 4 3 5 2 108.5300 4.4300e+02 3 6 9 2 109.5000 5.2000e+02 - 3 6 8 2 109.6000 4.5000e+02 3 6 7 2 109.6000 4.5000e+02 - 4 3 5 2 108.5300 4.4300e+02 - 6 9 10 2 109.5000 4.5000e+02 + 3 6 8 2 109.6000 4.5000e+02 + 5 3 6 2 109.6000 4.5000e+02 8 6 9 2 107.5700 4.8400e+02 + 6 9 10 2 109.5000 4.5000e+02 7 6 9 2 107.5700 4.8400e+02 7 6 8 2 108.5300 4.4300e+02 9 10 11 2 124.0000 7.3000e+02 9 10 12 2 115.0000 6.1000e+02 11 10 12 2 121.0000 6.8500e+02 - 10 12 20 2 120.0000 5.6000e+02 10 12 13 2 120.0000 5.6000e+02 + 10 12 20 2 120.0000 5.6000e+02 13 12 20 2 120.0000 5.6000e+02 - 12 20 18 2 120.0000 5.6000e+02 - 12 20 21 2 120.0000 5.0500e+02 12 13 14 2 120.0000 5.0500e+02 12 13 15 2 120.0000 5.6000e+02 + 12 20 21 2 120.0000 5.0500e+02 + 12 20 18 2 120.0000 5.6000e+02 + 13 15 16 2 120.0000 5.0500e+02 14 13 15 2 120.0000 5.0500e+02 13 15 17 2 120.0000 5.6000e+02 - 13 15 16 2 120.0000 5.0500e+02 - 16 15 17 2 120.0000 5.0500e+02 15 17 18 2 120.0000 5.6000e+02 15 17 22 2 120.0000 5.6000e+02 - 17 22 23 2 121.0000 6.8500e+02 + 16 15 17 2 120.0000 5.0500e+02 18 17 22 2 120.0000 5.6000e+02 - 17 22 24 2 115.0000 6.1000e+02 17 18 20 2 120.0000 5.6000e+02 17 18 19 2 120.0000 5.0500e+02 - 19 18 20 2 120.0000 5.0500e+02 + 17 22 24 2 115.0000 6.1000e+02 + 17 22 23 2 121.0000 6.8500e+02 18 20 21 2 120.0000 5.0500e+02 + 19 18 20 2 120.0000 5.0500e+02 23 22 24 2 124.0000 7.3000e+02 22 24 25 2 109.5000 4.5000e+02 24 25 27 2 107.5700 4.8400e+02 - 24 25 28 2 109.5000 5.2000e+02 24 25 26 2 107.5700 4.8400e+02 + 24 25 28 2 109.5000 5.2000e+02 27 25 28 2 109.6000 4.5000e+02 - 26 25 27 2 108.5300 4.4300e+02 - 26 25 28 2 109.6000 4.5000e+02 - 25 28 31 2 109.5000 5.2000e+02 25 28 29 2 109.6000 4.5000e+02 25 28 30 2 109.6000 4.5000e+02 + 26 25 28 2 109.6000 4.5000e+02 + 25 28 31 2 109.5000 5.2000e+02 + 26 25 27 2 108.5300 4.4300e+02 30 28 31 2 107.5700 4.8400e+02 29 28 30 2 108.5300 4.4300e+02 29 28 31 2 107.5700 4.8400e+02 28 31 32 2 109.5000 4.5000e+02 - 31 32 33 2 124.0000 7.3000e+02 31 32 34 2 115.0000 6.1000e+02 - 33 32 34 2 121.0000 6.8500e+02 + 31 32 33 2 124.0000 7.3000e+02 32 34 42 2 120.0000 5.6000e+02 32 34 35 2 120.0000 5.6000e+02 - 34 35 37 2 120.0000 5.6000e+02 - 35 34 42 2 120.0000 5.6000e+02 - 34 35 36 2 120.0000 5.0500e+02 + 33 32 34 2 121.0000 6.8500e+02 34 42 43 2 120.0000 5.0500e+02 + 35 34 42 2 120.0000 5.6000e+02 34 42 40 2 120.0000 5.6000e+02 - 36 35 37 2 120.0000 5.0500e+02 - 35 37 39 2 120.0000 5.6000e+02 + 34 35 36 2 120.0000 5.0500e+02 + 34 35 37 2 120.0000 5.6000e+02 35 37 38 2 120.0000 5.0500e+02 - 37 39 40 2 120.0000 5.6000e+02 + 35 37 39 2 120.0000 5.6000e+02 + 36 35 37 2 120.0000 5.0500e+02 37 39 44 2 120.0000 5.6000e+02 38 37 39 2 120.0000 5.0500e+02 - 39 44 46 2 115.0000 6.1000e+02 + 37 39 40 2 120.0000 5.6000e+02 40 39 44 2 120.0000 5.6000e+02 - 39 44 45 2 121.0000 6.8500e+02 - 39 40 41 2 120.0000 5.0500e+02 39 40 42 2 120.0000 5.6000e+02 + 39 40 41 2 120.0000 5.0500e+02 + 39 44 45 2 121.0000 6.8500e+02 + 39 44 46 2 115.0000 6.1000e+02 41 40 42 2 120.0000 5.0500e+02 40 42 43 2 120.0000 5.0500e+02 45 44 46 2 124.0000 7.3000e+02 44 46 47 2 109.5000 4.5000e+02 - 46 47 49 2 107.5700 4.8400e+02 - 46 47 48 2 107.5700 4.8400e+02 46 47 50 2 109.5000 5.2000e+02 + 46 47 48 2 107.5700 4.8400e+02 + 46 47 49 2 107.5700 4.8400e+02 + 47 50 53 2 109.5000 5.2000e+02 48 47 50 2 109.6000 4.5000e+02 - 48 47 49 2 108.5300 4.4300e+02 - 49 47 50 2 109.6000 4.5000e+02 47 50 52 2 109.6000 4.5000e+02 - 47 50 53 2 109.5000 5.2000e+02 47 50 51 2 109.6000 4.5000e+02 + 49 47 50 2 109.6000 4.5000e+02 + 48 47 49 2 108.5300 4.4300e+02 51 50 53 2 107.5700 4.8400e+02 - 51 50 52 2 108.5300 4.4300e+02 - 50 53 54 2 109.5000 4.5000e+02 52 50 53 2 107.5700 4.8400e+02 - 53 54 55 2 124.0000 7.3000e+02 + 50 53 54 2 109.5000 4.5000e+02 + 51 50 52 2 108.5300 4.4300e+02 53 54 56 2 115.0000 6.1000e+02 + 53 54 55 2 124.0000 7.3000e+02 55 54 56 2 121.0000 6.8500e+02 54 56 64 2 120.0000 5.6000e+02 54 56 57 2 120.0000 5.6000e+02 57 56 64 2 120.0000 5.6000e+02 56 57 58 2 120.0000 5.0500e+02 56 57 59 2 120.0000 5.6000e+02 - 56 64 62 2 120.0000 5.6000e+02 56 64 65 2 120.0000 5.0500e+02 + 56 64 62 2 120.0000 5.6000e+02 58 57 59 2 120.0000 5.0500e+02 - 57 59 61 2 120.0000 5.6000e+02 57 59 60 2 120.0000 5.0500e+02 - 59 61 62 2 120.0000 5.6000e+02 + 57 59 61 2 120.0000 5.6000e+02 60 59 61 2 120.0000 5.0500e+02 + 59 61 62 2 120.0000 5.6000e+02 59 61 66 2 120.0000 5.6000e+02 - 62 61 66 2 120.0000 5.6000e+02 - 61 66 68 2 115.0000 6.1000e+02 61 66 67 2 121.0000 6.8500e+02 - 61 62 64 2 120.0000 5.6000e+02 + 61 66 68 2 115.0000 6.1000e+02 + 62 61 66 2 120.0000 5.6000e+02 61 62 63 2 120.0000 5.0500e+02 - 63 62 64 2 120.0000 5.0500e+02 + 61 62 64 2 120.0000 5.6000e+02 62 64 65 2 120.0000 5.0500e+02 + 63 62 64 2 120.0000 5.0500e+02 67 66 68 2 124.0000 7.3000e+02 66 68 69 2 109.5000 4.5000e+02 - 68 69 70 2 107.5700 4.8400e+02 - 68 69 71 2 107.5700 4.8400e+02 68 69 72 2 109.5000 5.2000e+02 + 68 69 71 2 107.5700 4.8400e+02 + 68 69 70 2 107.5700 4.8400e+02 70 69 72 2 109.6000 4.5000e+02 70 69 71 2 108.5300 4.4300e+02 71 69 72 2 109.6000 4.5000e+02 69 72 73 2 109.6000 4.5000e+02 - 69 72 75 2 109.5000 5.2000e+02 69 72 74 2 109.6000 4.5000e+02 - 73 72 74 2 108.5300 4.4300e+02 + 69 72 75 2 109.5000 5.2000e+02 73 72 75 2 107.5700 4.8400e+02 - 72 75 76 2 109.5000 4.5000e+02 74 72 75 2 107.5700 4.8400e+02 + 72 75 76 2 109.5000 4.5000e+02 + 73 72 74 2 108.5300 4.4300e+02 75 76 77 2 124.0000 7.3000e+02 75 76 78 2 115.0000 6.1000e+02 77 76 78 2 121.0000 6.8500e+02 - 76 78 79 2 120.0000 5.6000e+02 76 78 86 2 120.0000 5.6000e+02 - 78 86 84 2 120.0000 5.6000e+02 - 78 86 87 2 120.0000 5.0500e+02 - 79 78 86 2 120.0000 5.6000e+02 + 76 78 79 2 120.0000 5.6000e+02 78 79 81 2 120.0000 5.6000e+02 78 79 80 2 120.0000 5.0500e+02 - 80 79 81 2 120.0000 5.0500e+02 + 79 78 86 2 120.0000 5.6000e+02 + 78 86 84 2 120.0000 5.6000e+02 + 78 86 87 2 120.0000 5.0500e+02 79 81 82 2 120.0000 5.0500e+02 + 80 79 81 2 120.0000 5.0500e+02 79 81 83 2 120.0000 5.6000e+02 82 81 83 2 120.0000 5.0500e+02 81 83 84 2 120.0000 5.6000e+02 81 83 88 2 120.0000 5.6000e+02 - 83 88 90 2 115.0000 6.1000e+02 - 83 88 89 2 121.0000 6.8500e+02 84 83 88 2 120.0000 5.6000e+02 83 84 86 2 120.0000 5.6000e+02 83 84 85 2 120.0000 5.0500e+02 + 83 88 90 2 115.0000 6.1000e+02 + 83 88 89 2 121.0000 6.8500e+02 85 84 86 2 120.0000 5.0500e+02 84 86 87 2 120.0000 5.0500e+02 88 90 91 2 109.5000 4.5000e+02 89 88 90 2 124.0000 7.3000e+02 90 91 92 2 107.5700 4.8400e+02 - 90 91 93 2 107.5700 4.8400e+02 90 91 94 2 109.5000 5.2000e+02 - 91 94 97 2 109.5000 5.2000e+02 + 90 91 93 2 107.5700 4.8400e+02 + 92 91 94 2 109.6000 4.5000e+02 93 91 94 2 109.6000 4.5000e+02 91 94 96 2 109.6000 4.5000e+02 91 94 95 2 109.6000 4.5000e+02 - 92 91 94 2 109.6000 4.5000e+02 + 91 94 97 2 109.5000 5.2000e+02 92 91 93 2 108.5300 4.4300e+02 95 94 96 2 108.5300 4.4300e+02 95 94 97 2 107.5700 4.8400e+02 @@ -654,14 +654,14 @@ E6SD 3 94 97 98 2 109.5000 4.5000e+02 97 98 99 2 124.0000 7.3000e+02 97 98 100 2 115.0000 6.1000e+02 + 98 100 108 2 120.0000 5.6000e+02 99 98 100 2 121.0000 6.8500e+02 98 100 101 2 120.0000 5.6000e+02 - 98 100 108 2 120.0000 5.6000e+02 - 100 108 106 2 120.0000 5.6000e+02 - 100 108 109 2 120.0000 5.0500e+02 101 100 108 2 120.0000 5.6000e+02 - 100 101 103 2 120.0000 5.6000e+02 100 101 102 2 120.0000 5.0500e+02 + 100 101 103 2 120.0000 5.6000e+02 + 100 108 106 2 120.0000 5.6000e+02 + 100 108 109 2 120.0000 5.0500e+02 102 101 103 2 120.0000 5.0500e+02 101 103 105 2 120.0000 5.6000e+02 101 103 104 2 120.0000 5.0500e+02 @@ -669,48 +669,48 @@ E6SD 3 103 105 106 2 120.0000 5.6000e+02 104 103 105 2 120.0000 5.0500e+02 105 106 107 2 120.0000 5.0500e+02 - 106 105 110 2 120.0000 5.6000e+02 105 106 108 2 120.0000 5.6000e+02 + 106 105 110 2 120.0000 5.6000e+02 105 110 112 2 115.0000 6.1000e+02 105 110 111 2 121.0000 6.8500e+02 107 106 108 2 120.0000 5.0500e+02 106 108 109 2 120.0000 5.0500e+02 - 110 112 113 2 109.5000 4.5000e+02 111 110 112 2 124.0000 7.3000e+02 - 112 113 116 2 109.5000 5.2000e+02 + 110 112 113 2 109.5000 4.5000e+02 112 113 115 2 107.5700 4.8400e+02 + 112 113 116 2 109.5000 5.2000e+02 112 113 114 2 107.5700 4.8400e+02 + 114 113 116 2 109.6000 4.5000e+02 113 116 118 2 109.6000 4.5000e+02 + 113 116 117 2 109.6000 4.5000e+02 113 116 119 2 109.5000 5.2000e+02 115 113 116 2 109.6000 4.5000e+02 - 113 116 117 2 109.6000 4.5000e+02 - 114 113 116 2 109.6000 4.5000e+02 114 113 115 2 108.5300 4.4300e+02 - 116 119 120 2 109.5000 4.5000e+02 + 117 116 118 2 108.5300 4.4300e+02 118 116 119 2 107.5700 4.8400e+02 117 116 119 2 107.5700 4.8400e+02 - 117 116 118 2 108.5300 4.4300e+02 + 116 119 120 2 109.5000 4.5000e+02 [ dihedrals ] -; GROMOS improper dihedrals +; improper dihedrals 10 9 11 12 2 0.0000 1.6736e+02 10 9 11 12 2 0.0000 1.6736e+02 12 10 13 20 2 0.0000 1.6736e+02 - 20 12 18 21 2 0.0000 1.6736e+02 13 12 14 15 2 0.0000 1.6736e+02 + 20 12 18 21 2 0.0000 1.6736e+02 15 13 16 17 2 0.0000 1.6736e+02 17 15 18 22 2 0.0000 1.6736e+02 - 22 17 23 24 2 0.0000 1.6736e+02 18 17 19 20 2 0.0000 1.6736e+02 + 22 17 23 24 2 0.0000 1.6736e+02 32 31 33 34 2 0.0000 1.6736e+02 32 31 33 34 2 0.0000 1.6736e+02 34 32 35 42 2 0.0000 1.6736e+02 - 35 34 36 37 2 0.0000 1.6736e+02 42 34 40 43 2 0.0000 1.6736e+02 + 35 34 36 37 2 0.0000 1.6736e+02 37 35 38 39 2 0.0000 1.6736e+02 39 37 40 44 2 0.0000 1.6736e+02 - 44 39 45 46 2 0.0000 1.6736e+02 40 39 41 42 2 0.0000 1.6736e+02 + 44 39 45 46 2 0.0000 1.6736e+02 54 53 55 56 2 0.0000 1.6736e+02 54 53 55 56 2 0.0000 1.6736e+02 56 54 57 64 2 0.0000 1.6736e+02 @@ -723,17 +723,17 @@ E6SD 3 76 75 77 78 2 0.0000 1.6736e+02 76 75 77 78 2 0.0000 1.6736e+02 78 76 79 86 2 0.0000 1.6736e+02 - 86 78 84 87 2 0.0000 1.6736e+02 79 78 80 81 2 0.0000 1.6736e+02 + 86 78 84 87 2 0.0000 1.6736e+02 81 79 82 83 2 0.0000 1.6736e+02 83 81 84 88 2 0.0000 1.6736e+02 - 88 83 89 90 2 0.0000 1.6736e+02 84 83 85 86 2 0.0000 1.6736e+02 + 88 83 89 90 2 0.0000 1.6736e+02 98 97 99 100 2 0.0000 1.6736e+02 98 97 99 100 2 0.0000 1.6736e+02 100 98 101 108 2 0.0000 1.6736e+02 - 108 100 106 109 2 0.0000 1.6736e+02 101 100 102 103 2 0.0000 1.6736e+02 + 108 100 106 109 2 0.0000 1.6736e+02 103 101 104 105 2 0.0000 1.6736e+02 105 103 106 110 2 0.0000 1.6736e+02 106 105 107 108 2 0.0000 1.6736e+02 @@ -744,10 +744,10 @@ E6SD 3 2 3 6 9 1 0.0000 5.9200e+00 3 3 6 9 10 1 0.0000 1.2600e+00 3 11 10 12 13 1 180.0000 5.8600e+00 2 - 13 12 20 18 1 180.0000 4.1800e+01 2 20 12 13 15 1 180.0000 4.1800e+01 2 - 17 18 20 12 1 180.0000 4.1800e+01 2 + 13 12 20 18 1 180.0000 4.1800e+01 2 12 13 15 17 1 180.0000 4.1800e+01 2 + 17 18 20 12 1 180.0000 4.1800e+01 2 13 15 17 18 1 180.0000 4.1800e+01 2 15 17 18 20 1 180.0000 4.1800e+01 2 15 17 22 23 1 180.0000 5.8600e+00 2 @@ -755,19 +755,19 @@ E6SD 3 24 25 28 31 1 0.0000 5.9200e+00 3 25 28 31 32 1 0.0000 1.2600e+00 3 33 32 34 35 1 180.0000 5.8600e+00 2 - 34 35 37 39 1 180.0000 4.1800e+01 2 - 42 34 35 37 1 180.0000 4.1800e+01 2 35 34 42 40 1 180.0000 4.1800e+01 2 + 42 34 35 37 1 180.0000 4.1800e+01 2 39 40 42 34 1 180.0000 4.1800e+01 2 + 34 35 37 39 1 180.0000 4.1800e+01 2 35 37 39 40 1 180.0000 4.1800e+01 2 - 37 39 40 42 1 180.0000 4.1800e+01 2 37 39 44 45 1 180.0000 5.8600e+00 2 + 37 39 40 42 1 180.0000 4.1800e+01 2 44 46 47 50 1 0.0000 1.2600e+00 3 46 47 50 53 1 0.0000 5.9200e+00 3 47 50 53 54 1 0.0000 1.2600e+00 3 55 54 56 57 1 180.0000 5.8600e+00 2 - 57 56 64 62 1 180.0000 4.1800e+01 2 64 56 57 59 1 180.0000 4.1800e+01 2 + 57 56 64 62 1 180.0000 4.1800e+01 2 56 57 59 61 1 180.0000 4.1800e+01 2 61 62 64 56 1 180.0000 4.1800e+01 2 57 59 61 62 1 180.0000 4.1800e+01 2 @@ -777,10 +777,10 @@ E6SD 3 68 69 72 75 1 0.0000 5.9200e+00 3 69 72 75 76 1 0.0000 1.2600e+00 3 77 76 78 79 1 180.0000 5.8600e+00 2 - 83 84 86 78 1 180.0000 4.1800e+01 2 - 79 78 86 84 1 180.0000 4.1800e+01 2 86 78 79 81 1 180.0000 4.1800e+01 2 78 79 81 83 1 180.0000 4.1800e+01 2 + 79 78 86 84 1 180.0000 4.1800e+01 2 + 83 84 86 78 1 180.0000 4.1800e+01 2 79 81 83 84 1 180.0000 4.1800e+01 2 81 83 84 86 1 180.0000 4.1800e+01 2 81 83 88 89 1 180.0000 5.8600e+00 2 @@ -789,9 +789,9 @@ E6SD 3 91 94 97 98 1 0.0000 1.2600e+00 3 99 98 100 101 1 180.0000 5.8600e+00 2 101 100 108 106 1 180.0000 4.1800e+01 2 - 105 106 108 100 1 180.0000 4.1800e+01 2 108 100 101 103 1 180.0000 4.1800e+01 2 100 101 103 105 1 180.0000 4.1800e+01 2 + 105 106 108 100 1 180.0000 4.1800e+01 2 101 103 105 106 1 180.0000 4.1800e+01 2 103 105 110 111 1 180.0000 5.8600e+00 2 103 105 106 108 1 180.0000 4.1800e+01 2 diff --git a/data_paper_examples/polyester.png b/data_paper_examples/polyester.png index 0bb9a0eb5c07fd72c1a98c4ffaf891c9a460e080..d1a8d293d92a5e7ac626906c6ddfa959ac3e29e4 100644 GIT binary patch delta 2874 zcmV-A3&r%?Q$ylkFxZe-!>k?anh(b7mYHbsC?g+32Wg>Am+?Q;P^UQb9;y zi_oA4NiLEi3QJrRwrEpOBq7*?UW?GV_YZp5rh=>}kXjf?git|kraJeZe`?(}y6|(( zz4Oiazw@2%EX1zNf}RXIHYA>nbT-pDVsjuwF+~v}O@`kecTh+rj1_IRf8_h$#^nG1 z-}Ud@Ko9o7HijGT_YM* 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z&W`iLW2Vr~+It!Ir_ouuR~<5iNB+{M_2(q3(JmLh)|hu@SPC8}DirgTd;DvX6`#d$ z-Aw&P51!77>XcKcfXs}vH`zxyK3!2KUxDBZTH&fUKk*l$&WIU8tK%93S$fE0ZvQ2B z2y3*$)aJ_Unj=fb*&aJ2MPh#Q z-b{J&Z11b3m&B)B`mmug6GfZHcMR8wJU=Y1^MBV2`>u6?=eZ|CjW(UGj1i$_W4eCp z_QQsEV^sKchhOJ^()QqCr$~Q%d_;4iEmdD%f9~YtNp1C1Vsfeo4Zq$i^~sTNQ9t%1 zja%ydU>VO;fujOupXt%)?@{w$y^_qF-Ewj{6Rbd|(+y61f@Uxi% zr=C^IQepolaqJVBc>CjVK2?FSgXUl*>j_6gwaQ~>$11~XyGwp9)g+7EgRb7Bi`|?o ztWAlN-myK2AMxT-Oq7a0#qhsgX;W*v(XwZjGmrPoihD zrAkHh^Y+qGp+E|iin#O*C7zle*hNHE%ybNv$i^QoC(ItMka@gMsd%X=DCKeKab>%Q zOwWIsNFED|JR2zca>Yx8L?{OM|mnnXd1@3~vV~2;aaI znImCtx@BoFYxY~eR+lNQ{zAF&yx-qP+mdg(|5Y1w)LU1TM^pKclAPxMt)Iqgia6Z7 zPjnW6hC#t&x94jtBOyiCH)kmRhk6vj=86;-bQPG|IvnM1S4$Su+r7iuNF`C0dgMZ+P^q#u zcQRR5XGl6c7`c@-O4p2;3d~QWn|R%xD$Q}$YTds>w1eu&)Gqfx?yTnZbQ5NbW>OFh zp}tS8h(XrOEiC$H*{}atuEc#EUyvpxaeb=%c06H%(X|uHa>1M=RX@E?ye{VDBLx&~ ztuRBDl*UgPeu9Cw$X>?l?|pok-#JRCr6Oc{|GADxqyXazz4f!6R31yBj9(E9VGjmv z>hlRst(`Wj@YQ9HU7dg1$XRca97gy z&5$0yu88$zi(g?>>3ozg?Pa|`28(cX{J|VN;be^Q3XS==HF=k+Z{4|{bqpbjNdHu5 z^3AEUO~23|fx(jdWES|neQB2mpnKk?nJr^Lsl Date: Wed, 5 Feb 2025 14:15:00 +1000 Subject: [PATCH 09/12] Add polymer extension test for polymer constructed from OPLS itp file originating topology monomers --- tests/test_polymer.py | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/tests/test_polymer.py b/tests/test_polymer.py index f59de57..0c67b5e 100644 --- a/tests/test_polymer.py +++ b/tests/test_polymer.py @@ -235,3 +235,30 @@ def test_multijoined_polymer(data_dir: Path, output_dir: Path): polymer_topology = polymer.topology polymer_topology.to_ITP(output_dir/'double_sugar_polymer.itp') Visualize.polymer(polymer,infer_bond_order=False).draw2D(output_dir/'double_sugar_polymer.png',(400,200)) + +def test_OPLS_polymer(data_dir: Path, output_dir: Path): + """ + This test is to make sure a Polymer constructed from OPLS ff monomers + extends without error + """ + top = Topology.from_ITP(data_dir/"OPLS_UNK_460A12.itp", format="opls") + + # Create a Junction to join 'to' and another to join 'from'. + # Provide the bonding atom and the leaving atom, in that order, for the + # Junction - they must have a bond between them. + to_j = Junction(top.get_atom("C02"), top.get_atom("C01"), name = "to") + from_j = Junction(top.get_atom("C03"), top.get_atom("C04"), name = "from") + + # Create a Monomer from the Topology and a list of the Junctions + monomer = Monomer(top, [to_j, from_j]) + + # Start the Polymer with one Monomer + polymer = Polymer(monomer) + + # Extend the Polymer to the desired length (in this case 20) + for i in range(29): + polymer.extend(monomer, from_junction_name="from", to_junction_name="to") + + # Save the polymer to a file and visualise the structure with RDKit for an easy visual structure check + polymer.topology.to_ITP(output_dir/'OPLS_30mer.itp') + Visualize.polymer(polymer,infer_bond_order=False).draw2D(output_dir/'OPLS_30mer.png',(400,300)) \ No newline at end of file From 81e808f95d0098fbc012481ac556a250830f31ce Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Thu, 6 Feb 2025 12:56:56 +1000 Subject: [PATCH 10/12] Add polymer extension test for polymer constructed from AMBER itp file originating topology monomers --- tests/data/AMBER_PNIPAM_extend.itp | 323 +++++++++++++++++++++++++++++ tests/polytop/test_polymer.py | 29 ++- 2 files changed, 351 insertions(+), 1 deletion(-) create mode 100644 tests/data/AMBER_PNIPAM_extend.itp diff --git a/tests/data/AMBER_PNIPAM_extend.itp b/tests/data/AMBER_PNIPAM_extend.itp new file mode 100644 index 0000000..3d3aec8 --- /dev/null +++ b/tests/data/AMBER_PNIPAM_extend.itp @@ -0,0 +1,323 @@ +[ atoms ] +; nr type resi res atom cgnr charge mass ; qtot bond_type + 1 c3 1 UNK C00 1 -0.092100 12.01000 ; qtot -0.092 + 2 c3 1 UNK C01 2 -0.079400 12.01000 ; qtot -0.171 + 3 c3 1 UNK C02 3 -0.072400 12.01000 ; qtot -0.244 + 4 c3 1 UNK C03 4 -0.127700 12.01000 ; qtot -0.372 + 5 c3 1 UNK C04 5 -0.072400 12.01000 ; qtot -0.444 + 6 c3 1 UNK C05 6 -0.099100 12.01000 ; qtot -0.543 + 7 c 1 UNK C06 7 0.661098 12.01000 ; qtot 0.118 + 8 o 1 UNK O07 8 -0.612100 16.00000 ; qtot -0.494 + 9 ns 1 UNK N08 9 -0.574900 14.01000 ; qtot -1.069 + 10 c3 1 UNK C09 10 0.095700 12.01000 ; qtot -0.973 + 11 c3 1 UNK C0A 11 -0.110100 12.01000 ; qtot -1.083 + 12 c3 1 UNK C0B 12 -0.110100 12.01000 ; qtot -1.194 + 13 hc 1 UNK H0C 13 0.034367 1.00800 ; qtot -1.159 + 14 hc 1 UNK H0D 14 0.034367 1.00800 ; qtot -1.125 + 15 hc 1 UNK H0E 15 0.034367 1.00800 ; qtot -1.090 + 16 hc 1 UNK H0F 16 0.036700 1.00800 ; qtot -1.054 + 17 hc 1 UNK H0G 17 0.036700 1.00800 ; qtot -1.017 + 18 hc 1 UNK H0H 18 0.059700 1.00800 ; qtot -0.957 + 19 hc 1 UNK H0I 19 0.059700 1.00800 ; qtot -0.898 + 20 hc 1 UNK H0J 20 0.056700 1.00800 ; qtot -0.841 + 21 hc 1 UNK H0K 21 0.040700 1.00800 ; qtot -0.800 + 22 hc 1 UNK H0M 22 0.040700 1.00800 ; qtot -0.760 + 23 hc 1 UNK H0N 23 0.042033 1.00800 ; qtot -0.717 + 24 hc 1 UNK H0O 24 0.042033 1.00800 ; qtot -0.675 + 25 hc 1 UNK H0P 25 0.042033 1.00800 ; qtot -0.633 + 26 hn 1 UNK H0Q 26 0.304500 1.00800 ; qtot -0.329 + 27 h1 1 UNK H0R 27 0.089700 1.00800 ; qtot -0.239 + 28 hc 1 UNK H0S 28 0.039867 1.00800 ; qtot -0.199 + 29 hc 1 UNK H0T 29 0.039867 1.00800 ; qtot -0.159 + 30 hc 1 UNK H0U 30 0.039867 1.00800 ; qtot -0.120 + 31 hc 1 UNK H0V 31 0.039867 1.00800 ; qtot -0.080 + 32 hc 1 UNK H0W 32 0.039867 1.00800 ; qtot -0.040 + 33 hc 1 UNK H0X 33 0.039867 1.00800 ; qtot 0.000 + +[ bonds ] +; ai aj funct r k + 1 2 1 1.5380e-01 1.9456e+05 ; C00 - C01 + 1 13 1 1.0970e-01 3.1455e+05 ; C00 - H0C + 1 14 1 1.0970e-01 3.1455e+05 ; C00 - H0D + 1 15 1 1.0970e-01 3.1455e+05 ; C00 - H0E + 2 3 1 1.5380e-01 1.9456e+05 ; C01 - C02 + 2 16 1 1.0970e-01 3.1455e+05 ; C01 - H0F + 2 17 1 1.0970e-01 3.1455e+05 ; C01 - H0G + 3 4 1 1.5380e-01 1.9456e+05 ; C02 - C03 + 3 18 1 1.0970e-01 3.1455e+05 ; C02 - H0H + 3 19 1 1.0970e-01 3.1455e+05 ; C02 - H0I + 4 5 1 1.5380e-01 1.9456e+05 ; C03 - C04 + 4 7 1 1.5240e-01 2.0351e+05 ; C03 - C06 + 4 20 1 1.0970e-01 3.1455e+05 ; C03 - H0J + 5 6 1 1.5380e-01 1.9456e+05 ; C04 - C05 + 5 21 1 1.0970e-01 3.1455e+05 ; C04 - H0K + 5 22 1 1.0970e-01 3.1455e+05 ; C04 - H0M + 6 23 1 1.0970e-01 3.1455e+05 ; C05 - H0N + 6 24 1 1.0970e-01 3.1455e+05 ; C05 - H0O + 6 25 1 1.0970e-01 3.1455e+05 ; C05 - H0P + 7 8 1 1.2180e-01 5.4610e+05 ; C06 - O07 + 7 9 1 1.3790e-01 2.9807e+05 ; C06 - N08 + 9 10 1 1.4620e-01 2.2075e+05 ; N08 - C09 + 9 26 1 1.0130e-01 4.4124e+05 ; N08 - H0Q + 10 11 1 1.5380e-01 1.9456e+05 ; C09 - C0A + 10 12 1 1.5380e-01 1.9456e+05 ; C09 - C0B + 10 27 1 1.0970e-01 3.1455e+05 ; C09 - H0R + 11 28 1 1.0970e-01 3.1455e+05 ; C0A - H0S + 11 29 1 1.0970e-01 3.1455e+05 ; C0A - H0T + 11 30 1 1.0970e-01 3.1455e+05 ; C0A - H0U + 12 31 1 1.0970e-01 3.1455e+05 ; C0B - H0V + 12 32 1 1.0970e-01 3.1455e+05 ; C0B - H0W + 12 33 1 1.0970e-01 3.1455e+05 ; C0B - H0X + +[ pairs ] +; ai aj funct + 1 4 1 ; C00 - C03 + 1 18 1 ; C00 - H0H + 1 19 1 ; C00 - H0I + 2 5 1 ; C01 - C04 + 2 7 1 ; C01 - C06 + 2 20 1 ; C01 - H0J + 3 6 1 ; C02 - C05 + 3 8 1 ; C02 - O07 + 3 9 1 ; C02 - N08 + 3 21 1 ; C02 - H0K + 3 22 1 ; C02 - H0M + 4 10 1 ; C03 - C09 + 4 16 1 ; C03 - H0F + 4 17 1 ; C03 - H0G + 4 23 1 ; C03 - H0N + 4 24 1 ; C03 - H0O + 4 25 1 ; C03 - H0P + 4 26 1 ; C03 - H0Q + 5 8 1 ; C04 - O07 + 5 9 1 ; C04 - N08 + 5 18 1 ; C04 - H0H + 5 19 1 ; C04 - H0I + 6 7 1 ; C05 - C06 + 6 20 1 ; C05 - H0J + 7 11 1 ; C06 - C0A + 7 12 1 ; C06 - C0B + 7 18 1 ; C06 - H0H + 7 19 1 ; C06 - H0I + 7 21 1 ; C06 - H0K + 7 22 1 ; C06 - H0M + 7 27 1 ; C06 - H0R + 8 10 1 ; O07 - C09 + 8 20 1 ; O07 - H0J + 8 26 1 ; O07 - H0Q + 9 20 1 ; N08 - H0J + 9 28 1 ; N08 - H0S + 9 29 1 ; N08 - H0T + 9 30 1 ; N08 - H0U + 9 31 1 ; N08 - H0V + 9 32 1 ; N08 - H0W + 9 33 1 ; N08 - H0X + 11 26 1 ; C0A - H0Q + 11 31 1 ; C0A - H0V + 11 32 1 ; C0A - H0W + 11 33 1 ; C0A - H0X + 12 26 1 ; C0B - H0Q + 12 28 1 ; C0B - H0S + 12 29 1 ; C0B - H0T + 12 30 1 ; C0B - H0U + 13 3 1 ; H0C - C02 + 13 16 1 ; H0C - H0F + 13 17 1 ; H0C - H0G + 14 3 1 ; H0D - C02 + 14 16 1 ; H0D - H0F + 14 17 1 ; H0D - H0G + 15 3 1 ; H0E - C02 + 15 16 1 ; H0E - H0F + 15 17 1 ; H0E - H0G + 16 18 1 ; H0F - H0H + 16 19 1 ; H0F - H0I + 17 18 1 ; H0G - H0H + 17 19 1 ; H0G - H0I + 18 20 1 ; H0H - H0J + 19 20 1 ; H0I - H0J + 20 21 1 ; H0J - H0K + 20 22 1 ; H0J - H0M + 21 23 1 ; H0K - H0N + 21 24 1 ; H0K - H0O + 21 25 1 ; H0K - H0P + 22 23 1 ; H0M - H0N + 22 24 1 ; H0M - H0O + 22 25 1 ; H0M - H0P + 26 27 1 ; H0Q - H0R + 27 28 1 ; H0R - H0S + 27 29 1 ; H0R - H0T + 27 30 1 ; H0R - H0U + 27 31 1 ; H0R - H0V + 27 32 1 ; H0R - H0W + 27 33 1 ; H0R - H0X + +[ angles ] +; ai aj ak funct theta cth + 1 2 3 1 1.1151e+02 5.4308e+02 ; C00 - C01 - C02 + 1 2 16 1 1.0980e+02 3.9162e+02 ; C00 - C01 - H0F + 1 2 17 1 1.0980e+02 3.9162e+02 ; C00 - C01 - H0G + 2 1 13 1 1.0980e+02 3.9162e+02 ; C01 - C00 - H0C + 2 1 14 1 1.0980e+02 3.9162e+02 ; C01 - C00 - H0D + 2 1 15 1 1.0980e+02 3.9162e+02 ; C01 - C00 - H0E + 2 3 4 1 1.1151e+02 5.4308e+02 ; C01 - C02 - C03 + 2 3 18 1 1.0980e+02 3.9162e+02 ; C01 - C02 - H0H + 2 3 19 1 1.0980e+02 3.9162e+02 ; C01 - C02 - H0I + 3 2 16 1 1.0980e+02 3.9162e+02 ; C02 - C01 - H0F + 3 2 17 1 1.0980e+02 3.9162e+02 ; C02 - C01 - H0G + 3 4 5 1 1.1151e+02 5.4308e+02 ; C02 - C03 - C04 + 3 4 7 1 1.1104e+02 5.4643e+02 ; C02 - C03 - C06 + 3 4 20 1 1.0980e+02 3.9162e+02 ; C02 - C03 - H0J + 4 3 18 1 1.0980e+02 3.9162e+02 ; C03 - C02 - H0H + 4 3 19 1 1.0980e+02 3.9162e+02 ; C03 - C02 - H0I + 4 5 6 1 1.1151e+02 5.4308e+02 ; C03 - C04 - C05 + 4 5 21 1 1.0980e+02 3.9162e+02 ; C03 - C04 - H0K + 4 5 22 1 1.0980e+02 3.9162e+02 ; C03 - C04 - H0M + 4 7 8 1 1.2320e+02 7.0793e+02 ; C03 - C06 - O07 + 4 7 9 1 1.1518e+02 7.0542e+02 ; C03 - C06 - N08 + 5 4 7 1 1.1104e+02 5.4643e+02 ; C04 - C03 - C06 + 5 4 20 1 1.0980e+02 3.9162e+02 ; C04 - C03 - H0J + 5 6 23 1 1.0980e+02 3.9162e+02 ; C04 - C05 - H0N + 5 6 24 1 1.0980e+02 3.9162e+02 ; C04 - C05 - H0O + 5 6 25 1 1.0980e+02 3.9162e+02 ; C04 - C05 - H0P + 6 5 21 1 1.0980e+02 3.9162e+02 ; C05 - C04 - H0K + 6 5 22 1 1.0980e+02 3.9162e+02 ; C05 - C04 - H0M + 7 4 20 1 1.0877e+02 3.9664e+02 ; C06 - C03 - H0J + 7 9 10 1 1.2069e+02 5.4643e+02 ; C06 - N08 - C09 + 7 9 26 1 1.1755e+02 4.0752e+02 ; C06 - N08 - H0Q + 8 7 9 1 1.2305e+02 9.5228e+02 ; O07 - C06 - N08 + 9 10 11 1 1.1161e+02 6.9622e+02 ; N08 - C09 - C0A + 9 10 12 1 1.1161e+02 6.9622e+02 ; N08 - C09 - C0B + 9 10 27 1 1.0888e+02 5.1463e+02 ; N08 - C09 - H0R + 10 9 26 1 1.1768e+02 3.8576e+02 ; C09 - N08 - H0Q + 10 11 28 1 1.0980e+02 3.9162e+02 ; C09 - C0A - H0S + 10 11 29 1 1.0980e+02 3.9162e+02 ; C09 - C0A - H0T + 10 11 30 1 1.0980e+02 3.9162e+02 ; C09 - C0A - H0U + 10 12 31 1 1.0980e+02 3.9162e+02 ; C09 - C0B - H0V + 10 12 32 1 1.0980e+02 3.9162e+02 ; C09 - C0B - H0W + 10 12 33 1 1.0980e+02 3.9162e+02 ; C09 - C0B - H0X + 11 10 12 1 1.1151e+02 5.4308e+02 ; C0A - C09 - C0B + 11 10 27 1 1.0956e+02 3.9246e+02 ; C0A - C09 - H0R + 12 10 27 1 1.0956e+02 3.9246e+02 ; C0B - C09 - H0R + 13 1 14 1 1.0758e+02 3.2635e+02 ; H0C - C00 - H0D + 13 1 15 1 1.0758e+02 3.2635e+02 ; H0C - C00 - H0E + 14 1 15 1 1.0758e+02 3.2635e+02 ; H0D - C00 - H0E + 16 2 17 1 1.0758e+02 3.2635e+02 ; H0F - C01 - H0G + 18 3 19 1 1.0758e+02 3.2635e+02 ; H0H - C02 - H0I + 21 5 22 1 1.0758e+02 3.2635e+02 ; H0K - C04 - H0M + 23 6 24 1 1.0758e+02 3.2635e+02 ; H0N - C05 - H0O + 23 6 25 1 1.0758e+02 3.2635e+02 ; H0N - C05 - H0P + 24 6 25 1 1.0758e+02 3.2635e+02 ; H0O - C05 - H0P + 28 11 29 1 1.0758e+02 3.2635e+02 ; H0S - C0A - H0T + 28 11 30 1 1.0758e+02 3.2635e+02 ; H0S - C0A - H0U + 29 11 30 1 1.0758e+02 3.2635e+02 ; H0T - C0A - H0U + 31 12 32 1 1.0758e+02 3.2635e+02 ; H0V - C0B - H0W + 31 12 33 1 1.0758e+02 3.2635e+02 ; H0V - C0B - H0X + 32 12 33 1 1.0758e+02 3.2635e+02 ; H0W - C0B - H0X + +[ dihedrals ] ; propers +; for gromacs 4.5 or higher, using funct 9 +; i j k l func phase kd pn + 1 2 3 4 9 0.00 0.46024 1 ; C00- C01- C02- C03 + 1 2 3 4 9 0.00 0.54392 3 ; C00- C01- C02- C03 + 1 2 3 4 9 180.00 1.21336 2 ; C00- C01- C02- C03 + 1 2 3 18 9 0.00 0.33472 3 ; C00- C01- C02- H0H + 1 2 3 19 9 0.00 0.33472 3 ; C00- C01- C02- H0I + 2 3 4 5 9 0.00 0.46024 1 ; C01- C02- C03- C04 + 2 3 4 5 9 0.00 0.54392 3 ; C01- C02- C03- C04 + 2 3 4 5 9 180.00 1.21336 2 ; C01- C02- C03- C04 + 2 3 4 7 9 0.00 0.41840 3 ; C01- C02- C03- C06 + 2 3 4 20 9 0.00 0.33472 3 ; C01- C02- C03- H0J + 3 4 5 6 9 0.00 0.46024 1 ; C02- C03- C04- C05 + 3 4 5 6 9 0.00 0.54392 3 ; C02- C03- C04- C05 + 3 4 5 6 9 180.00 1.21336 2 ; C02- C03- C04- C05 + 3 4 5 21 9 0.00 0.33472 3 ; C02- C03- C04- H0K + 3 4 5 22 9 0.00 0.33472 3 ; C02- C03- C04- H0M + 3 4 7 8 9 0.00 3.09616 1 ; C02- C03- C06- O07 + 3 4 7 8 9 180.00 1.12968 2 ; C02- C03- C06- O07 + 3 4 7 8 9 180.00 2.30120 3 ; C02- C03- C06- O07 + 3 4 7 9 9 180.00 0.00000 4 ; C02- C03- C06- N08 + 3 4 7 9 9 180.00 2.97064 2 ; C02- C03- C06- N08 + 4 3 2 16 9 0.00 0.33472 3 ; C03- C02- C01- H0F + 4 3 2 17 9 0.00 0.33472 3 ; C03- C02- C01- H0G + 4 5 6 23 9 0.00 0.33472 3 ; C03- C04- C05- H0N + 4 5 6 24 9 0.00 0.33472 3 ; C03- C04- C05- H0O + 4 5 6 25 9 0.00 0.33472 3 ; C03- C04- C05- H0P + 4 7 9 10 9 0.00 2.09200 1 ; C03- C06- N08- C09 + 4 7 9 10 9 180.00 1.08784 2 ; C03- C06- N08- C09 + 4 7 9 26 9 180.00 10.46000 2 ; C03- C06- N08- H0Q + 5 4 3 18 9 0.00 0.33472 3 ; C04- C03- C02- H0H + 5 4 3 19 9 0.00 0.33472 3 ; C04- C03- C02- H0I + 5 4 7 8 9 0.00 3.09616 1 ; C04- C03- C06- O07 + 5 4 7 8 9 180.00 1.12968 2 ; C04- C03- C06- O07 + 5 4 7 8 9 180.00 2.30120 3 ; C04- C03- C06- O07 + 5 4 7 9 9 180.00 0.00000 4 ; C04- C03- C06- N08 + 5 4 7 9 9 180.00 2.97064 2 ; C04- C03- C06- N08 + 6 5 4 7 9 0.00 0.41840 3 ; C05- C04- C03- C06 + 6 5 4 20 9 0.00 0.33472 3 ; C05- C04- C03- H0J + 7 4 3 18 9 0.00 0.65084 3 ; C06- C03- C02- H0H + 7 4 3 19 9 0.00 0.65084 3 ; C06- C03- C02- H0I + 7 4 5 21 9 0.00 0.65084 3 ; C06- C03- C04- H0K + 7 4 5 22 9 0.00 0.65084 3 ; C06- C03- C04- H0M + 7 9 10 11 9 0.00 0.71128 3 ; C06- N08- C09- C0A + 7 9 10 11 9 180.00 0.41840 4 ; C06- N08- C09- C0A + 7 9 10 11 9 180.00 4.26768 1 ; C06- N08- C09- C0A + 7 9 10 12 9 0.00 0.71128 3 ; C06- N08- C09- C0B + 7 9 10 12 9 180.00 0.41840 4 ; C06- N08- C09- C0B + 7 9 10 12 9 180.00 4.26768 1 ; C06- N08- C09- C0B + 7 9 10 27 9 180.00 0.00000 2 ; C06- N08- C09- H0R + 8 7 4 20 9 0.00 3.47272 1 ; O07- C06- C03- H0J + 8 7 4 20 9 180.00 0.16736 3 ; O07- C06- C03- H0J + 8 7 9 10 9 180.00 10.46000 2 ; O07- C06- N08- C09 + 8 7 9 26 9 0.00 8.36800 1 ; O07- C06- N08- H0Q + 8 7 9 26 9 180.00 10.46000 2 ; O07- C06- N08- H0Q + 9 7 4 20 9 180.00 0.00000 2 ; N08- C06- C03- H0J + 9 10 11 28 9 0.00 0.65084 3 ; N08- C09- C0A- H0S + 9 10 11 29 9 0.00 0.65084 3 ; N08- C09- C0A- H0T + 9 10 11 30 9 0.00 0.65084 3 ; N08- C09- C0A- H0U + 9 10 12 31 9 0.00 0.65084 3 ; N08- C09- C0B- H0V + 9 10 12 32 9 0.00 0.65084 3 ; N08- C09- C0B- H0W + 9 10 12 33 9 0.00 0.65084 3 ; N08- C09- C0B- H0X + 11 10 9 26 9 0.00 0.00000 0 ; C0A- C09- N08- H0Q + 11 10 12 31 9 0.00 0.33472 3 ; C0A- C09- C0B- H0V + 11 10 12 32 9 0.00 0.33472 3 ; C0A- C09- C0B- H0W + 11 10 12 33 9 0.00 0.33472 3 ; C0A- C09- C0B- H0X + 12 10 9 26 9 0.00 0.00000 0 ; C0B- C09- N08- H0Q + 12 10 11 28 9 0.00 0.33472 3 ; C0B- C09- C0A- H0S + 12 10 11 29 9 0.00 0.33472 3 ; C0B- C09- C0A- H0T + 12 10 11 30 9 0.00 0.33472 3 ; C0B- C09- C0A- H0U + 13 1 2 3 9 0.00 0.33472 3 ; H0C- C00- C01- C02 + 13 1 2 16 9 0.00 0.50208 3 ; H0C- C00- C01- H0F + 13 1 2 17 9 0.00 0.50208 3 ; H0C- C00- C01- H0G + 14 1 2 3 9 0.00 0.33472 3 ; H0D- C00- C01- C02 + 14 1 2 16 9 0.00 0.50208 3 ; H0D- C00- C01- H0F + 14 1 2 17 9 0.00 0.50208 3 ; H0D- C00- C01- H0G + 15 1 2 3 9 0.00 0.33472 3 ; H0E- C00- C01- C02 + 15 1 2 16 9 0.00 0.50208 3 ; H0E- C00- C01- H0F + 15 1 2 17 9 0.00 0.50208 3 ; H0E- C00- C01- H0G + 16 2 3 18 9 0.00 0.50208 3 ; H0F- C01- C02- H0H + 16 2 3 19 9 0.00 0.50208 3 ; H0F- C01- C02- H0I + 17 2 3 18 9 0.00 0.50208 3 ; H0G- C01- C02- H0H + 17 2 3 19 9 0.00 0.50208 3 ; H0G- C01- C02- H0I + 18 3 4 20 9 0.00 0.50208 3 ; H0H- C02- C03- H0J + 19 3 4 20 9 0.00 0.50208 3 ; H0I- C02- C03- H0J + 20 4 5 21 9 0.00 0.50208 3 ; H0J- C03- C04- H0K + 20 4 5 22 9 0.00 0.50208 3 ; H0J- C03- C04- H0M + 21 5 6 23 9 0.00 0.50208 3 ; H0K- C04- C05- H0N + 21 5 6 24 9 0.00 0.50208 3 ; H0K- C04- C05- H0O + 21 5 6 25 9 0.00 0.50208 3 ; H0K- C04- C05- H0P + 22 5 6 23 9 0.00 0.50208 3 ; H0M- C04- C05- H0N + 22 5 6 24 9 0.00 0.50208 3 ; H0M- C04- C05- H0O + 22 5 6 25 9 0.00 0.50208 3 ; H0M- C04- C05- H0P + 26 9 10 27 9 0.00 0.00000 0 ; H0Q- N08- C09- H0R + 27 10 11 28 9 0.00 0.65084 3 ; H0R- C09- C0A- H0S + 27 10 11 29 9 0.00 0.65084 3 ; H0R- C09- C0A- H0T + 27 10 11 30 9 0.00 0.65084 3 ; H0R- C09- C0A- H0U + 27 10 12 31 9 0.00 0.65084 3 ; H0R- C09- C0B- H0V + 27 10 12 32 9 0.00 0.65084 3 ; H0R- C09- C0B- H0W + 27 10 12 33 9 0.00 0.65084 3 ; H0R- C09- C0B- H0X + +[ dihedrals ] ; impropers +; treated as propers in GROMACS to use correct AMBER analytical function +; i j k l func phase kd pn + 4 9 7 8 4 180.00 43.93200 2 ; C03- N08- C06- O07 + 7 10 9 26 4 180.00 4.60240 2 ; C06- C09- N08- H0Q diff --git a/tests/polytop/test_polymer.py b/tests/polytop/test_polymer.py index 0c67b5e..1782393 100644 --- a/tests/polytop/test_polymer.py +++ b/tests/polytop/test_polymer.py @@ -261,4 +261,31 @@ def test_OPLS_polymer(data_dir: Path, output_dir: Path): # Save the polymer to a file and visualise the structure with RDKit for an easy visual structure check polymer.topology.to_ITP(output_dir/'OPLS_30mer.itp') - Visualize.polymer(polymer,infer_bond_order=False).draw2D(output_dir/'OPLS_30mer.png',(400,300)) \ No newline at end of file + Visualize.polymer(polymer,infer_bond_order=False).draw2D(output_dir/'OPLS_30mer.png',(400,300)) + +def test_AMBER_polymer(data_dir: Path, output_dir: Path): + """ + This test is to make sure a Polymer constructed from OPLS ff monomers + extends without error + """ + top = Topology.from_ITP(data_dir/"AMBER_PNIPAM_extend.itp", format="amber") + + # Create a Junction to join 'to' and another to join 'from'. + # Provide the bonding atom and the leaving atom, in that order, for the + # Junction - they must have a bond between them. + to_j = Junction(top.get_atom("C02"), top.get_atom("C01"), name = "to") + from_j = Junction(top.get_atom("C03"), top.get_atom("C04"), name = "from") + + # Create a Monomer from the Topology and a list of the Junctions + monomer = Monomer(top, [to_j, from_j]) + + # Start the Polymer with one Monomer + polymer = Polymer(monomer) + + # Extend the Polymer to the desired length (in this case 20) + for i in range(29): + polymer.extend(monomer, from_junction_name="from", to_junction_name="to") + + # Save the polymer to a file and visualise the structure with RDKit for an easy visual structure check + polymer.topology.to_ITP(output_dir/'AMBER_30mer.itp') + Visualize.polymer(polymer,infer_bond_order=False).draw2D(output_dir/'AMBER_30mer.png',(400,300)) \ No newline at end of file From c0db921912a8ebec3c6da993009d075ce87f05a5 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Thu, 6 Feb 2025 13:10:14 +1000 Subject: [PATCH 11/12] Update docstring in Polytop.Polymer.extend() to inform users that they should only extend a Polymer with a Monomer of the same format (e.g. gromos-gromos, NOT gromos-amber) --- polytop/polytop/Polymer.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/polytop/polytop/Polymer.py b/polytop/polytop/Polymer.py index 9583c21..df5b674 100644 --- a/polytop/polytop/Polymer.py +++ b/polytop/polytop/Polymer.py @@ -186,6 +186,11 @@ def extend(self, monomer, from_junction_name: str, to_junction_name: str, keep_c Dihedrals are correct. For best results: + * Do NOT extend a Polymer of a given format (e.g. gromos), with a + Monomer of a different format (e.g. AMBER). This is not recommended as + it is not the supported functionality and has NOT been tested. PolyTop + may crash, produce an incorrect Polymer Topology or behave in an + undefined manner. * Provide topologies where all atoms that will be lost have a partial charge of 0. This will ensure the charge of each atom in the resulting Polymer is identical to it's charge in the provided Monomer it came from. From 142ea1068c3d0794a4373eb241010e0f77c14096 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Fri, 7 Feb 2025 14:14:21 +1000 Subject: [PATCH 12/12] Add polymer extension test for polymer constructed from CHARMM itp file originating topology monomers. Modified the __str__ representation choice in Angle to ensure output itp is correct and writes without error, and how the 'missing' bond attributes in CHARMM ff itp's are stored in a Bond to enable extend() to work. --- polytop/polytop/Angles.py | 3 +- polytop/polytop/Bonds.py | 4 +- tests/data/CHARMM_PNIPAM_extend.itp | 302 ++++++++++++++++++++++++++++ tests/polytop/test_polymer.py | 31 ++- 4 files changed, 335 insertions(+), 5 deletions(-) create mode 100644 tests/data/CHARMM_PNIPAM_extend.itp diff --git a/polytop/polytop/Angles.py b/polytop/polytop/Angles.py index 1a537f9..2285814 100644 --- a/polytop/polytop/Angles.py +++ b/polytop/polytop/Angles.py @@ -175,7 +175,8 @@ def remove(self): self.bond_bc.angles.remove(self) def __str__(self): - if self.format == "charmm": + # TODO: figure out why topology.to_ITP is causing Angles to write as a different format + if self.format == "charmm" or self.angle_value==None and self.force_constant==None: return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.angle_type:>5}" else: return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.angle_type:>5} {self.angle_value:>10.4f} {self.force_constant:.4e}" diff --git a/polytop/polytop/Bonds.py b/polytop/polytop/Bonds.py index 438a115..2c0e4f1 100644 --- a/polytop/polytop/Bonds.py +++ b/polytop/polytop/Bonds.py @@ -86,8 +86,8 @@ def from_line(cls, line: str, atoms: List["Atom"], format: str = "gromos") -> Bo atom_b = atoms[int(parts[1]) - 1] bond_type = int(parts[2]) if format=="charmm": - bond_length = None - force_constant = None + bond_length = 0 # 0 instead of None enables extend to work, is not saved to output + force_constant = 0 else: bond_length = float(parts[3]) force_constant = float(parts[4]) diff --git a/tests/data/CHARMM_PNIPAM_extend.itp b/tests/data/CHARMM_PNIPAM_extend.itp new file mode 100644 index 0000000..d2edb3f --- /dev/null +++ b/tests/data/CHARMM_PNIPAM_extend.itp @@ -0,0 +1,302 @@ +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 PNI rtp PNI q +0.0 + 1 CG331 1 PNI C1 1 -0.273 12.011 ; qtot -0.273 + 2 CG321 1 PNI C2 2 -0.191 12.011 ; qtot -0.191 + 3 CG321 1 PNI C3 3 -0.247 12.011 ; qtot -0.247 + 4 CG311 1 PNI C4 4 0.133 12.011 ; qtot 0.133 + 5 CG321 1 PNI C5 5 -0.223 12.011 ; qtot -0.223 + 6 CG331 1 PNI C6 6 -0.303 12.011 ; qtot -0.303 + 7 CG2O1 1 PNI C7 7 0.507 12.011 ; qtot 0.507 + 8 OG2D1 1 PNI O8 8 -0.517 15.9994 ; qtot -0.517 + 9 NG2S1 1 PNI N9 9 -0.492 14.007 ; qtot -0.492 + 10 CG311 1 PNI C10 10 0.021 12.011 ; qtot 0.021 + 11 CG331 1 PNI C11 11 -0.269 12.011 ; qtot -0.269 + 12 CG331 1 PNI C12 12 -0.269 12.011 ; qtot -0.269 + 13 HGA3 1 PNI H13 13 0.09 1.008 ; qtot 0.09 + 14 HGA3 1 PNI H14 14 0.09 1.008 ; qtot 0.09 + 15 HGA3 1 PNI H15 15 0.09 1.008 ; qtot 0.09 + 16 HGA2 1 PNI H16 16 0.09 1.008 ; qtot 0.09 + 17 HGA2 1 PNI H17 17 0.09 1.008 ; qtot 0.09 + 18 HGA2 1 PNI H18 18 0.09 1.008 ; qtot 0.09 + 19 HGA2 1 PNI H19 19 0.09 1.008 ; qtot 0.09 + 20 HGA1 1 PNI H20 20 0.09 1.008 ; qtot 0.09 + 21 HGA2 1 PNI H21 21 0.09 1.008 ; qtot 0.09 + 22 HGA2 1 PNI H22 22 0.09 1.008 ; qtot 0.09 + 23 HGA3 1 PNI H23 23 0.09 1.008 ; qtot 0.09 + 24 HGA3 1 PNI H24 24 0.09 1.008 ; qtot 0.09 + 25 HGA3 1 PNI H25 25 0.09 1.008 ; qtot 0.09 + 26 HGP1 1 PNI H26 26 0.323 1.008 ; qtot 0.323 + 27 HGA1 1 PNI H27 27 0.09 1.008 ; qtot 0.09 + 28 HGA3 1 PNI H28 28 0.09 1.008 ; qtot 0.09 + 29 HGA3 1 PNI H29 29 0.09 1.008 ; qtot 0.09 + 30 HGA3 1 PNI H30 30 0.09 1.008 ; qtot 0.09 + 31 HGA3 1 PNI H31 31 0.09 1.008 ; qtot 0.09 + 32 HGA3 1 PNI H32 32 0.09 1.008 ; qtot 0.09 + 33 HGA3 1 PNI H33 33 0.09 1.008 ; qtot 0.09 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 13 1 1 + 17 2 1 + 16 2 1 + 21 5 1 + 2 1 1 + 2 3 1 + 1 15 1 + 1 14 1 + 24 6 1 + 5 22 1 + 5 6 1 + 5 4 1 + 20 4 1 + 6 23 1 + 6 25 1 + 3 4 1 + 3 18 1 + 3 19 1 + 4 7 1 + 26 9 1 + 7 9 1 + 7 8 1 + 9 10 1 + 28 11 1 + 31 12 1 + 10 11 1 + 10 12 1 + 10 27 1 + 29 11 1 + 33 12 1 + 11 30 1 + 12 32 1 + +[ pairs ] +; ai aj funct c0 c1 c2 c3 + 1 4 1 + 1 18 1 + 1 19 1 + 2 5 1 + 2 7 1 + 2 20 1 + 3 6 1 + 3 8 1 + 3 9 1 + 3 13 1 + 3 14 1 + 3 15 1 + 3 21 1 + 3 22 1 + 4 10 1 + 4 16 1 + 4 17 1 + 4 23 1 + 4 24 1 + 4 25 1 + 4 26 1 + 5 8 1 + 5 9 1 + 5 18 1 + 5 19 1 + 6 7 1 + 6 20 1 + 7 11 1 + 7 12 1 + 7 18 1 + 7 19 1 + 7 21 1 + 7 22 1 + 7 27 1 + 8 10 1 + 8 20 1 + 8 26 1 + 9 20 1 + 9 28 1 + 9 29 1 + 9 30 1 + 9 31 1 + 9 32 1 + 9 33 1 + 11 26 1 + 11 31 1 + 11 32 1 + 11 33 1 + 12 26 1 + 12 28 1 + 12 29 1 + 12 30 1 + 13 16 1 + 13 17 1 + 14 16 1 + 14 17 1 + 15 16 1 + 15 17 1 + 16 18 1 + 16 19 1 + 17 18 1 + 17 19 1 + 18 20 1 + 19 20 1 + 20 21 1 + 20 22 1 + 21 23 1 + 21 24 1 + 21 25 1 + 22 23 1 + 22 24 1 + 22 25 1 + 26 27 1 + 27 28 1 + 27 29 1 + 27 30 1 + 27 31 1 + 27 32 1 + 27 33 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 13 1 2 5 + 13 1 15 5 + 13 1 14 5 + 2 1 15 5 + 2 1 14 5 + 15 1 14 5 + 17 2 16 5 + 17 2 1 5 + 17 2 3 5 + 16 2 1 5 + 16 2 3 5 + 1 2 3 5 + 2 3 4 5 + 2 3 18 5 + 2 3 19 5 + 4 3 18 5 + 4 3 19 5 + 18 3 19 5 + 5 4 20 5 + 5 4 3 5 + 5 4 7 5 + 20 4 3 5 + 20 4 7 5 + 3 4 7 5 + 21 5 22 5 + 21 5 6 5 + 21 5 4 5 + 22 5 6 5 + 22 5 4 5 + 6 5 4 5 + 24 6 5 5 + 24 6 23 5 + 24 6 25 5 + 5 6 23 5 + 5 6 25 5 + 23 6 25 5 + 4 7 9 5 + 4 7 8 5 + 9 7 8 5 + 26 9 7 5 + 26 9 10 5 + 7 9 10 5 + 9 10 11 5 + 9 10 12 5 + 9 10 27 5 + 11 10 12 5 + 11 10 27 5 + 12 10 27 5 + 28 11 10 5 + 28 11 29 5 + 28 11 30 5 + 10 11 29 5 + 10 11 30 5 + 29 11 30 5 + 31 12 10 5 + 31 12 33 5 + 31 12 32 5 + 10 12 33 5 + 10 12 32 5 + 33 12 32 5 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 17 2 1 13 9 + 17 2 1 15 9 + 17 2 1 14 9 + 16 2 1 13 9 + 16 2 1 15 9 + 16 2 1 14 9 + 3 2 1 13 9 + 3 2 1 15 9 + 3 2 1 14 9 + 17 2 3 4 9 + 17 2 3 18 9 + 17 2 3 19 9 + 16 2 3 4 9 + 16 2 3 18 9 + 16 2 3 19 9 + 1 2 3 4 9 + 1 2 3 18 9 + 1 2 3 19 9 + 21 5 6 24 9 + 21 5 6 23 9 + 21 5 6 25 9 + 22 5 6 24 9 + 22 5 6 23 9 + 22 5 6 25 9 + 4 5 6 24 9 + 4 5 6 23 9 + 4 5 6 25 9 + 21 5 4 20 9 + 21 5 4 3 9 + 21 5 4 7 9 + 22 5 4 20 9 + 22 5 4 3 9 + 22 5 4 7 9 + 6 5 4 20 9 + 6 5 4 3 9 + 6 5 4 7 9 + 2 3 4 5 9 + 2 3 4 20 9 + 2 3 4 7 9 + 18 3 4 5 9 + 18 3 4 20 9 + 18 3 4 7 9 + 19 3 4 5 9 + 19 3 4 20 9 + 19 3 4 7 9 + 5 4 7 9 9 + 5 4 7 8 9 + 20 4 7 9 9 + 20 4 7 8 9 + 3 4 7 9 9 + 3 4 7 8 9 + 4 7 9 26 9 + 4 7 9 10 9 + 8 7 9 26 9 + 8 7 9 10 9 + 26 9 10 11 9 + 26 9 10 12 9 + 26 9 10 27 9 + 7 9 10 11 9 + 7 9 10 12 9 + 7 9 10 27 9 + 9 10 11 28 9 + 9 10 11 29 9 + 9 10 11 30 9 + 12 10 11 28 9 + 12 10 11 29 9 + 12 10 11 30 9 + 27 10 11 28 9 + 27 10 11 29 9 + 27 10 11 30 9 + 9 10 12 31 9 + 9 10 12 33 9 + 9 10 12 32 9 + 11 10 12 31 9 + 11 10 12 33 9 + 11 10 12 32 9 + 27 10 12 31 9 + 27 10 12 33 9 + 27 10 12 32 9 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 7 4 9 8 2 diff --git a/tests/polytop/test_polymer.py b/tests/polytop/test_polymer.py index 1782393..681a840 100644 --- a/tests/polytop/test_polymer.py +++ b/tests/polytop/test_polymer.py @@ -265,7 +265,7 @@ def test_OPLS_polymer(data_dir: Path, output_dir: Path): def test_AMBER_polymer(data_dir: Path, output_dir: Path): """ - This test is to make sure a Polymer constructed from OPLS ff monomers + This test is to make sure a Polymer constructed from AMBER ff monomers extends without error """ top = Topology.from_ITP(data_dir/"AMBER_PNIPAM_extend.itp", format="amber") @@ -288,4 +288,31 @@ def test_AMBER_polymer(data_dir: Path, output_dir: Path): # Save the polymer to a file and visualise the structure with RDKit for an easy visual structure check polymer.topology.to_ITP(output_dir/'AMBER_30mer.itp') - Visualize.polymer(polymer,infer_bond_order=False).draw2D(output_dir/'AMBER_30mer.png',(400,300)) \ No newline at end of file + Visualize.polymer(polymer,infer_bond_order=False).draw2D(output_dir/'AMBER_30mer.png',(400,300)) + +def test_CHARMM_polymer(data_dir: Path, output_dir: Path): + """ + This test is to make sure a Polymer constructed from CHARMM ff monomers + extends without error + """ + top = Topology.from_ITP(data_dir/"CHARMM_PNIPAM_extend.itp", format="charmm") + + # Create a Junction to join 'to' and another to join 'from'. + # Provide the bonding atom and the leaving atom, in that order, for the + # Junction - they must have a bond between them. + to_j = Junction(top.get_atom("C2"), top.get_atom("C1"), name = "to") + from_j = Junction(top.get_atom("C3"), top.get_atom("C4"), name = "from") + + # Create a Monomer from the Topology and a list of the Junctions + monomer = Monomer(top, [to_j, from_j]) + + # Start the Polymer with one Monomer + polymer = Polymer(monomer) + + # Extend the Polymer to the desired length (in this case 20) + for i in range(29): + polymer.extend(monomer, from_junction_name="from", to_junction_name="to") + + # Save the polymer to a file and visualise the structure with RDKit for an easy visual structure check + polymer.topology.to_ITP(output_dir/'CHARMM_30mer.itp') + Visualize.polymer(polymer,infer_bond_order=False).draw2D(output_dir/'CHARMM_30mer.png',(400,300)) \ No newline at end of file